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Last updated: 2024-07-17

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Knit directory: CocaineIVSA_RNASequencing_mDANeurons/

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Microglia contribute to methamphetamine reinforcement and reflect persistent transcriptional and morphological adaptations to the drug

Samara J. Vilca1,2†, Alexander V. Margetts1-3†, Isabella Fleites1-3, Claes R. Wahlestedt1-3 & Luis M. Tuesta1-3*

1 Department of Psychiatry & Behavioral Sciences 2 Center for Therapeutic Innovation 3 Sylvester Comprehensive Cancer Center University of Miami Miller School of Medicine, Miami, FL 33136 † Denotes equal contribution * Corresponding author (ltuesta@miami.edu)

1 Abstract

Abstract Methamphetamine use disorder (MUD) is a chronic, relapsing disease that is characterized by repeated drug use despite negative consequences for which there are currently no FDA approved cessation therapeutics. Repeated methamphetamine (METH) use induces long-term gene expression changes in brain regions associated with reward processing and drug-seeking behavior, and recent evidence suggests that methamphetamine-induced neuroinflammation may also shape behavioral and molecular responses to the drug. Microglia, the resident immune cells in the brain, are principal drivers of neuroinflammatory responses and contribute to the pathophysiology of substance use disorders. Here, we investigated transcriptional and morphological changes in striatal microglia in response to methamphetamine-taking and during methamphetamine abstinence, as well as their functional contribution to drug-taking behavior. We show that methamphetamine self-administration induces transcriptional changes related to protein folding, mRNA processing, immune signaling, and neurotransmission in striatal microglia. Importantly, many of these transcriptional changes persist through abstinence, a finding supported by morphological analysis. Functionally, we report that microglial ablation increases methamphetamine-taking, possibly involving neuroimmune and neurotransmitter regulation. In contrast, microglial depletion did not alter methamphetamine-seeking behavior following 21 days of abstinence, highlighting the complexity of drug-seeking behaviors. Taken together, these results suggest that methamphetamine induces both short and long-term changes in striatal microglia that contribute to altered drug-taking behavior and may be leveraged for preclinical development of methamphetamine cessation therapeutics.

2 DESeq2 Analysis

2.1 Setup

Building DESeq2 input files from gene count matrices output by StringTie following removal of samples that are outliers.

Running DeSeq2 analysis with factor levels of FoodTrained vs Maintenance, Craving vs Maintenance and Craving vs Foodtrained

3 Plot Estimates and Gather Results

3.1 Gather Results

These results include overview for each result file and dispersion estimates based on count values.

3.1.1 Craving vs FoodTraining

Craving vs FoodTrained CIVSA Results Overview

	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
Mrpl15|Mrpl15	2162.26767	0.3962276	0.3468265	1.1424376	0.2532722	0.9784152
Gm39587|Gm39587	20.30129	-2.1136742	3.3911278	-0.6232954	0.5330904	0.9997970
Lypla1|Lypla1	994.90242	0.0198799	0.8799100	0.0225931	0.9819748	0.9997970
Xkr4|Xkr4	4459.42848	-0.0337912	0.2715766	-0.1244260	0.9009780	0.9997970
Gm39585|Gm39585	5797.38480	0.0861245	0.2414588	0.3566843	0.7213282	0.9997970
Tcea1|Tcea1	2657.79689	-0.4037632	0.3330614	-1.2122786	0.2254058	0.9485680
Rgs20|Rgs20	422.79650	-0.1889366	0.7619761	-0.2479561	0.8041684	0.9997970
Gm16041|Gm16041	21.30106	7.5945314	3.6799019	2.0637864	0.0390380	0.6410945
Atp6v1h|Atp6v1h	10659.10495	-0.4956230	0.2967682	-1.6700675	0.0949060	0.8425404
LOC108167788|LOC108167788	11.33585	-0.8220772	3.4983015	-0.2349933	0.8142140	0.9997970
Npbwr1|Npbwr1	924.87540	-0.3079659	0.6636912	-0.4640199	0.6426335	0.9997970
Oprk1|Oprk1	15661.74234	-0.1442457	0.3231485	-0.4463757	0.6553259	0.9997970
St18|St18	279.69289	-2.0082890	0.9250037	-2.1711146	0.0299225	0.5845690
Rb1cc1|Rb1cc1	12217.86115	-0.0796796	0.2844821	-0.2800866	0.7794110	0.9997970
4732440D04Rik|4732440D04Rik	5369.16278	-0.4918180	0.2427412	-2.0261004	0.0427545	0.6632640
Gm26901|Gm26901	163.46252	-0.2293404	0.9562622	-0.2398300	0.8104620	0.9997970
Pcmtd1|Pcmtd1	4321.05905	0.2034726	0.2645104	0.7692425	0.4417494	0.9997970
Rrs1|Rrs1	625.86245	-0.4850563	0.6605362	-0.7343371	0.4627433	0.9997970
Mybl1|Mybl1	184.22714	1.4451732	1.2066675	1.1976566	0.2310507	0.9561403
Adhfe1|Adhfe1	452.68051	-0.1536903	0.7879557	-0.1950494	0.8453543	0.9997970

out of 23922 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 250, 1% LFC < 0 (down) : 48, 0.2% outliers [1] : 2272, 9.5% low counts [2] : 1352, 5.7% (mean count < 2) [1] see ‘cooksCutoff’ argument of ?results [2] see ‘independentFiltering’ argument of ?results

3.1.2 Maintenance vs FoodTraining

Craving vs FoodTrained CIVSA Results Overview

	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
Mrpl15|Mrpl15	2162.26767	0.6589546	0.3707556	1.7773286	0.0755142	0.3782100
Gm39587|Gm39587	20.30129	-1.7619611	3.6258386	-0.4859458	0.6270056	0.9345721
Lypla1|Lypla1	994.90242	0.0914200	0.9407122	0.0971817	0.9225821	0.9949371
Xkr4|Xkr4	4459.42848	0.6341912	0.2902594	2.1849118	0.0288953	0.2180911
Gm39585|Gm39585	5797.38480	1.1798031	0.2580070	4.5727554	0.0000048	0.0001973
Tcea1|Tcea1	2657.79689	0.1319203	0.3560044	0.3705581	0.7109667	0.9583981
Rgs20|Rgs20	422.79650	0.3482376	0.8144256	0.4275868	0.6689520	0.9469053
Gm16041|Gm16041	21.30106	7.1396504	3.9105846	1.8257246	0.0678918	0.3580246
Atp6v1h|Atp6v1h	10659.10495	0.1185235	0.3172387	0.3736100	0.7086945	0.9576220
LOC108167788|LOC108167788	11.33585	-0.5355535	3.7403736	-0.1431818	0.8861466	0.9949371
Npbwr1|Npbwr1	924.87540	-0.6449281	0.7097813	-0.9086292	0.3635459	0.7811879
Oprk1|Oprk1	15661.74234	0.2927281	0.3454541	0.8473720	0.3967878	0.8053124
St18|St18	279.69289	-1.0473877	0.9882176	-1.0598756	0.2892012	0.7120102
Rb1cc1|Rb1cc1	12217.86115	0.3066224	0.3041177	1.0082359	0.3133412	0.7348823
4732440D04Rik|4732440D04Rik	5369.16278	-0.1463996	0.2594995	-0.5641616	0.5726441	0.9132695
Gm26901|Gm26901	163.46252	-0.7535570	1.0236447	-0.7361509	0.4616389	0.8511309
Pcmtd1|Pcmtd1	4321.05905	0.5461501	0.2827538	1.9315391	0.0534164	0.3103856
Rrs1|Rrs1	625.86245	-0.1126443	0.7061219	-0.1595253	0.8732551	0.9949371
Mybl1|Mybl1	184.22714	-2.0915101	1.2989231	-1.6101878	0.1073569	0.4493503
Adhfe1|Adhfe1	452.68051	-1.0496649	0.8432838	-1.2447350	0.2132292	0.6256462

out of 23922 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 628, 2.6% LFC < 0 (down) : 1046, 4.4% outliers [1] : 2272, 9.5% low counts [2] : 2713, 11% (mean count < 6) [1] see ‘cooksCutoff’ argument of ?results [2] see ‘independentFiltering’ argument of ?results

3.1.3 Craving vs Maintenance

Craving vs Maintenance CIVSA Results Overview

	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
Mrpl15|Mrpl15	2162.26767	-0.2627261	0.3466449	-0.7579115	0.4485040	0.8651323
Gm39587|Gm39587	20.30129	-0.3516955	3.3976607	-0.1035111	0.9175574	0.9939251
Lypla1|Lypla1	994.90242	-0.0715356	0.8799222	-0.0812976	0.9352053	0.9951721
Xkr4|Xkr4	4459.42848	-0.6679818	0.2714805	-2.4605151	0.0138738	0.1495170
Gm39585|Gm39585	5797.38480	-1.0936780	0.2412810	-4.5327985	0.0000058	0.0002749
Tcea1|Tcea1	2657.79689	-0.5356827	0.3330620	-1.6083574	0.1077569	0.4613839
Rgs20|Rgs20	422.79650	-0.5371710	0.7618243	-0.7051114	0.4807409	0.8833096
Gm16041|Gm16041	21.30106	0.4549475	3.4906011	0.1303350	0.8963014	0.9909408
Atp6v1h|Atp6v1h	10659.10495	-0.6141458	0.2967693	-2.0694383	0.0385050	0.2733236
LOC108167788|LOC108167788	11.33585	-0.2865007	3.5020543	-0.0818093	0.9347983	0.9951721
Npbwr1|Npbwr1	924.87540	0.3369643	0.6640179	0.5074627	0.6118302	0.9372345
Oprk1|Oprk1	15661.74234	-0.4369729	0.3231413	-1.3522657	0.1762903	0.5932565
St18|St18	279.69289	-0.9608973	0.9259208	-1.0377748	0.2993749	0.7560424
Rb1cc1|Rb1cc1	12217.86115	-0.3863013	0.2844705	-1.3579665	0.1744743	0.5910084
4732440D04Rik|4732440D04Rik	5369.16278	-0.3454179	0.2427896	-1.4227046	0.1548218	0.5589467
Gm26901|Gm26901	163.46252	0.5242196	0.9577914	0.5473213	0.5841580	0.9274722
Pcmtd1|Pcmtd1	4321.05905	-0.3426769	0.2644209	-1.2959526	0.1949918	0.6240924
Rrs1|Rrs1	625.86245	-0.3724096	0.6606702	-0.5636845	0.5729689	0.9244236
Mybl1|Mybl1	184.22714	3.5366832	1.2149336	2.9110094	0.0036026	0.0603776
Adhfe1|Adhfe1	452.68051	0.8959769	0.7889411	1.1356702	0.2560946	0.7074992

out of 23922 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 1084, 4.5% LFC < 0 (down) : 324, 1.4% outliers [1] : 2271, 9.5% low counts [2] : 2713, 11% (mean count < 6) [1] see ‘cooksCutoff’ argument of ?results [2] see ‘independentFiltering’ argument of ?results

3.2 Annotate Results Files and Pull Significant DEGs

This subsection is for annotation the results files to include all necessary information for downstream analyses.

After annotation I subset the results to only view the significantly differentially expressed genes with an adjusted p-value > 0.05.

## Subset for significant genes only
results_sig <- subset(res, padj < 0.05)
results_sig2 <- subset(res2, padj < 0.05)
results_sig3 <- subset(res3, padj < 0.05)

3.2.1 Craving vs FoodTrained

Significant DEGs Craving vs FoodTrained

	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	symbol	description	entrez	ensembl
Gm28836|Gm28836	24.57062	18.512895	3.6825760	5.027159	0.0000005	0.0000748	Gm28836	predicted gene 28836	102635593	NA
Vwa3b|Vwa3b	68.09876	9.322079	2.2726944	4.101774	0.0000410	0.0048096	Vwa3b	von Willebrand factor A domain containing 3B	70853	ENSMUSG0….
4930439A04Rik|4930439A04Rik	239.71050	6.086391	1.0543294	5.772760	0.0000000	0.0000025	4930439A04Rik	RIKEN cDNA 4930439A04 gene	78119	NA
LOC108167622|LOC108167622	55.54376	21.271643	2.7752955	7.664641	0.0000000	0.0000000	LOC108167622	NA	NA
Pard3bos2|Pard3bos2	48.12983	-22.863164	3.6323379	-6.294338	0.0000000	0.0000002	Pard3bos2	par-3 family cell polarity regulator beta, opposite strand 2	105243940	ENSMUSG0….
Col4a3|Col4a3	29.96706	19.601203	3.5629545	5.501390	0.0000000	0.0000079	Col4a3	collagen, type IV, alpha 3	12828	ENSMUSG0….
Dnajb3|Dnajb3	70.36681	9.093523	2.0877638	4.355628	0.0000133	0.0017489	Dnajb3	DnaJ heat shock protein family (Hsp40) member B3	15504	ENSMUSG0….
Asb18|Asb18	12.85015	18.822115	3.6835623	5.109759	0.0000003	0.0000497	Asb18	ankyrin repeat and SOCS box-containing 18	208372	ENSMUSG0….
Gm41920|Gm41920	91.39199	20.766926	3.6195797	5.737386	0.0000000	0.0000030	Gm41920	predicted gene, 41920	105246666	NA
LOC105246710|LOC105246710	41.29964	21.372039	3.6789651	5.809253	0.0000000	0.0000022	LOC105246710	NA	NA
LOC108167732|LOC108167732	59.78860	21.982685	3.2366754	6.791749	0.0000000	0.0000000	LOC108167732	NA	NA
Fam129a|Fam129a	58.26340	9.542099	2.6179113	3.644928	0.0002675	0.0256134	Fam129a	NA	NA
Fmo1|Fmo1	51.26689	21.615385	2.7780474	7.780783	0.0000000	0.0000000	Fmo1	flavin containing monooxygenase 1	14261	ENSMUSG0….
Gorab|Gorab	666.84329	2.774594	0.5327144	5.208407	0.0000002	0.0000307	Gorab	golgin, RAB6-interacting	98376	ENSMUSG0….
Dnah14|Dnah14	41.60299	21.334681	3.4180513	6.241767	0.0000000	0.0000003	Dnah14	dynein, axonemal, heavy chain 14	240960	ENSMUSG0….
Atf3|Atf3	433.56152	-2.808330	0.7372279	-3.809311	0.0001394	0.0145805	Atf3	activating transcription factor 3	11910	ENSMUSG0….
B230208H11Rik|B230208H11Rik	48.28040	21.761939	2.7106546	8.028297	0.0000000	0.0000000	B230208H11Rik	RIKEN cDNA B230208H11 gene	320273	ENSMUSG0….
LOC108167797|LOC108167797	82.55280	9.456510	2.0988898	4.505482	0.0000066	0.0009335	LOC108167797	NA	NA
Fam26f|Fam26f	45.72461	21.035286	2.7780345	7.572003	0.0000000	0.0000000	Fam26f	NA	NA
Mical1|Mical1	109.45019	10.585487	2.6621850	3.976240	0.0000700	0.0077657	Mical1	microtubule associated monooxygenase, calponin and LIM domain containing 1	171580	ENSMUSG0….

3.2.2 Maintenance vs FoodTrained

Significant DEGs Maintenance vs FoodTrained

	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	symbol	description	entrez	ensembl
Gm39585|Gm39585	5797.38480	1.179803	0.2580070	4.572755	0.0000048	0.0001973	Gm39585	predicted gene, 39585	105243853	NA
Snhg6|Snhg6	522.81858	1.260214	0.4234933	2.975758	0.0029227	0.0446701	Snhg6	small nucleolar RNA host gene 6	73824	ENSMUSG0….
Trpa1|Trpa1	47.61966	-22.462571	3.6001396	-6.239361	0.0000000	0.0000001	Trpa1	transient receptor potential cation channel, subfamily A, member 1	277328	ENSMUSG0….
Rpl7|Rpl7	2486.96588	1.005240	0.3038678	3.308150	0.0009391	0.0184408	Rpl7	ribosomal protein L7	19989	ENSMUSG0….
Gm28836|Gm28836	24.57062	20.693225	3.9082681	5.294730	0.0000001	0.0000064	Gm28836	predicted gene 28836	102635593	NA
Gm32790|Gm32790	44.07127	9.563380	2.2173604	4.312957	0.0000161	0.0005913	Gm32790	predicted gene, 32790	102635458	NA
Fer1l5|Fer1l5	230.33092	-2.687277	0.8236933	-3.262473	0.0011044	0.0209149	Fer1l5	fer-1-like 5 (C. elegans)	100534273	ENSMUSG0….
Sema4c|Sema4c	1298.41081	-1.822125	0.6102459	-2.985887	0.0028276	0.0434624	Sema4c	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	20353	ENSMUSG0….
Vwa3b|Vwa3b	68.09876	8.717777	2.3896076	3.648204	0.0002641	0.0065801	Vwa3b	von Willebrand factor A domain containing 3B	70853	ENSMUSG0….
4930439A04Rik|4930439A04Rik	239.71050	7.561383	1.1113671	6.803677	0.0000000	0.0000000	4930439A04Rik	RIKEN cDNA 4930439A04 gene	78119	NA
Il1r2|Il1r2	73.49166	9.935852	2.8549805	3.480182	0.0005011	0.0112029	Il1r2	interleukin 1 receptor, type II	16178	ENSMUSG0….
Il1rl2|Il1rl2	153.74171	-24.241136	3.7848523	-6.404777	0.0000000	0.0000000	Il1rl2	interleukin 1 receptor-like 2	107527	ENSMUSG0….
LOC108167622|LOC108167622	55.54376	21.760261	2.9333442	7.418244	0.0000000	0.0000000	LOC108167622	NA	NA
Gm10561|Gm10561	31.31746	-8.823060	2.8132289	-3.136275	0.0017111	0.0295377	Gm10561	predicted gene 10561	628004	NA
Clk1|Clk1	11902.12420	1.056339	0.3336618	3.165897	0.0015461	0.0272603	Clk1	CDC-like kinase 1	12747	ENSMUSG0….
Stradb|Stradb	1233.07664	1.338207	0.3402418	3.933107	0.0000839	0.0024506	Stradb	STE20-related kinase adaptor beta	227154	ENSMUSG0….
Fam117b|Fam117b	1077.36822	1.740967	0.5934892	2.933444	0.0033522	0.0491723	Fam117b	family with sequence similarity 117, member B	72750	ENSMUSG0….
D230017M19Rik|D230017M19Rik	353.30341	1.817985	0.5121487	3.549721	0.0003856	0.0090159	D230017M19Rik	RIKEN cDNA D230017M19 gene	320933	NA
Arpc2|Arpc2	3532.07869	-1.115469	0.2391510	-4.664286	0.0000031	0.0001315	Arpc2	actin related protein 2/3 complex, subunit 2	76709	ENSMUSG0….
Cnppd1|Cnppd1	1597.07545	-1.205071	0.3232300	-3.728214	0.0001928	0.0049685	Cnppd1	cyclin Pas1/PHO80 domain containing 1	69171	ENSMUSG0….

3.2.3 Craving vs Maintenance

Significant Craving vs Maintenance

	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	symbol	description	entrez	ensembl
Gm39585|Gm39585	5797.38480	-1.0936780	0.2412810	-4.532799	0.0000058	0.0002749	Gm39585	predicted gene, 39585	105243853	NA
Trpa1|Trpa1	47.61966	20.0711689	3.3932805	5.914975	0.0000000	0.0000004	Trpa1	transient receptor potential cation channel, subfamily A, member 1	277328	ENSMUSG0….
Rpl7|Rpl7	2486.96588	-1.0763933	0.2841797	-3.787721	0.0001520	0.0049557	Rpl7	ribosomal protein L7	19989	ENSMUSG0….
1700001G17Rik|1700001G17Rik	704.98525	1.5933623	0.4255143	3.744557	0.0001807	0.0056755	1700001G17Rik	RIKEN cDNA 1700001G17 gene	67503	ENSMUSG0….
Fer1l5|Fer1l5	230.33092	2.7365069	0.7714625	3.547168	0.0003894	0.0105650	Fer1l5	fer-1-like 5 (C. elegans)	100534273	ENSMUSG0….
Sema4c|Sema4c	1298.41081	1.9826591	0.5709143	3.472779	0.0005151	0.0131477	Sema4c	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	20353	ENSMUSG0….
Il1rl2|Il1rl2	153.74171	22.2736364	3.5649386	6.247972	0.0000000	0.0000001	Il1rl2	interleukin 1 receptor-like 2	107527	ENSMUSG0….
Fam126b|Fam126b	8348.97120	-0.8264248	0.2373035	-3.482565	0.0004966	0.0127789	Fam126b	NA	NA
Pard3bos2|Pard3bos2	48.12983	-23.7390363	3.6316177	-6.536766	0.0000000	0.0000000	Pard3bos2	par-3 family cell polarity regulator beta, opposite strand 2	105243940	ENSMUSG0….
Zdbf2|Zdbf2	3291.47772	-0.9550029	0.3014901	-3.167610	0.0015370	0.0313656	Zdbf2	zinc finger, DBF-type containing 2	73884	ENSMUSG0….
Klf7|Klf7	3114.99312	-0.6650793	0.2115799	-3.143396	0.0016700	0.0335025	Klf7	Kruppel-like factor 7 (ubiquitous)	93691	ENSMUSG0….
Map2|Map2	15113.61849	-0.6774675	0.1781094	-3.803658	0.0001426	0.0047204	Map2	microtubule-associated protein 2	17756	ENSMUSG0….
Gm31047|Gm31047	43.06422	19.1697461	3.6817645	5.206674	0.0000002	0.0000130	Gm31047	predicted gene, 31047	102633145	NA
Arpc2|Arpc2	3532.07869	0.7956339	0.2237915	3.555246	0.0003776	0.0103047	Arpc2	actin related protein 2/3 complex, subunit 2	76709	ENSMUSG0….
Cnppd1|Cnppd1	1597.07545	0.9103462	0.3024970	3.009439	0.0026173	0.0473299	Cnppd1	cyclin Pas1/PHO80 domain containing 1	69171	ENSMUSG0….
Dnajb2|Dnajb2	1487.62355	1.1910673	0.3095799	3.847366	0.0001194	0.0040449	Dnajb2	DnaJ heat shock protein family (Hsp40) member B2	56812	ENSMUSG0….
Atg9a|Atg9a	8813.08524	2.0179237	0.4649911	4.339704	0.0000143	0.0006226	Atg9a	autophagy related 9A	245860	ENSMUSG0….
Resp18|Resp18	56768.10866	-0.8522294	0.2302091	-3.701980	0.0002139	0.0065238	Resp18	regulated endocrine-specific protein 18	19711	ENSMUSG0….
Chpf|Chpf	11304.97381	2.0829961	0.3845635	5.416520	0.0000001	0.0000049	Chpf	chondroitin polymerizing factor	74241	ENSMUSG0….
Tmem198|Tmem198	3311.19558	1.5407766	0.3702558	4.161384	0.0000316	0.0012693	Tmem198	transmembrane protein 198	319998	ENSMUSG0….

3.3 Visualize Shrinkage Estimations

Following subsetting, I want to see how the data looks based on effect size so I have run a shrinkage model using the “apeglm” method which normalizes counts based on effect size without major changes to data structure. I have included non-shrunk models as well for comparison.

3.3.1 Non-Shrunken L2FC

3.3.1.1 Craving vs FoodTrained

Past versions of "Non-Shrunken Estimate Plots-1.png"

Version	Author	Date
dc04b15	avm27	2024-07-17

3.3.1.2 Maintenance vs FoodTrained

Past versions of "Non-Shrunken Estimate Plots2-1.png"

Version	Author	Date
dc04b15	avm27	2024-07-17

3.3.1.3 Craving vs Maintenance

Past versions of "Non-Shrunken Estimate Plots3-1.png"

Version	Author	Date
dc04b15	avm27	2024-07-17

3.3.2 Shrunken L2FC

3.3.2.1 Craving vs FoodTrained

Past versions of "Shrunken Estimate Plots-1.png"

Version	Author	Date
dc04b15	avm27	2024-07-17

3.3.2.2 Maintenance vs FoodTrained

Past versions of "Shrunken Estimate Plots2-1.png"

Version	Author	Date
dc04b15	avm27	2024-07-17

3.3.2.3 Craving vs Maintenance

Past versions of "Shrunken Estimate Plots3-1.png"

Version	Author	Date
dc04b15	avm27	2024-07-17

4 Looking at Differentially Expressed Genes

We can generate a matrix to identify where our differentially expressed genes lie between each group based on an alpha value of 0.05.

## Matrix Visualizaattion
x <- vsDEGMatrix(
  data = dds, padj = 0.05, d.factor = "condition",
  type = "deseq", title = TRUE, legend = TRUE, grid = TRUE
)

Past versions of "Matrix of Differentially Expressed genes across groups-1.png"

Version	Author	Date
dc04b15	avm27	2024-07-17

5 Data Visualization

5.1 Normalized Counts and Plots of Genes of Interest

level_order <- c("FoodTrained", "Maintenance", "Craving") # this vector might be useful for other plots/analyses

normalized_counts <- counts(dds, normalized = TRUE)

5.1.1 Grin1

#### Grin1

d2 <- plotCounts(dds,
  gene = "Grin1|Grin1", intgroup = "condition",
  returnData = TRUE
)

a <- ggplot(d2, aes(x = factor(condition, level = level_order), y = count, color = condition)) +
  geom_point(position = position_jitter(w = 0.1, h = 0), size = 5) +
  scale_color_manual(values=c("#0000FF", "#FF8000", "#AD07E3")) +
  theme_bw() +
  xlab("Condition")+
  ylab("Normalized Counts")+
  ggtitle(
    label = "Grin1 Expression",
    subtitle = "Normalized Gene Expression"
  )

a

Past versions of "Selected Genes-1.png"

Version	Author	Date
a1c090c	avm27	2024-07-17
dc04b15	avm27	2024-07-17

5.1.2 Gabbr1

#### Gabbr1


d2 <- plotCounts(dds,
  gene = "Gabbr1|Gabbr1", intgroup = "condition",
  returnData = TRUE
)

a <- ggplot(d2, aes(x = factor(condition, level = level_order), y = count, color = condition)) +
  geom_point(position = position_jitter(w = 0.1, h = 0), size = 5) +
  scale_color_manual(values=c("#0000FF", "#FF8000", "#AD07E3")) +
  theme_bw() +
  xlab("Condition")+
  ylab("Normalized Counts")+
  ggtitle(
    label = "Gabbr1 Expression",
    subtitle = "Normalized Gene Expression"
  )

a

Past versions of "Selected Genes2-1.png"

Version	Author	Date
a1c090c	avm27	2024-07-17
dc04b15	avm27	2024-07-17

5.1.3 Th

#### Th


d2 <- plotCounts(dds,
  gene = "Th|Th", intgroup = "condition",
  returnData = TRUE
)

a <- ggplot(d2, aes(x = factor(condition, level = level_order), y = count, color = condition)) +
  geom_point(position = position_jitter(w = 0.1, h = 0), size = 5) +
  scale_color_manual(values=c("#0000FF", "#FF8000", "#AD07E3")) +
  theme_bw() +
  xlab("Condition")+
  ylab("Normalized Counts")+
  ggtitle(
    label = "Th Expression",
    subtitle = "Normalized Gene Expression"
  )

a

Past versions of "Selected Genes3-1.png"

Version	Author	Date
a1c090c	avm27	2024-07-17
dc04b15	avm27	2024-07-17

5.1.4 Ehmt2

#### Ehmt2

d2 <- plotCounts(dds,
  gene = "Ehmt2|Ehmt2", intgroup = "condition",
  returnData = TRUE
)

a <- ggplot(d2, aes(x = factor(condition, level = level_order), y = count, color = condition)) +
  geom_point(position = position_jitter(w = 0.1, h = 0), size = 5) +
  scale_color_manual(values=c("#0000FF", "#FF8000", "#AD07E3")) +
  theme_bw() +
  xlab("Condition")+
  ylab("Normalized Counts")+
  ggtitle(
    label = "Ehmt2 Expression",
    subtitle = "Normalized Gene Expression"
  )

a

Past versions of "Selected Genes4-1.png"

Version	Author	Date
a1c090c	avm27	2024-07-17
dc04b15	avm27	2024-07-17

5.1.5 Setdb1

#### Setdb1

d2 <- plotCounts(dds,
  gene = "Setdb1|Setdb1", intgroup = "condition",
  returnData = TRUE
)

a <- ggplot(d2, aes(x = factor(condition, level = level_order), y = count, color = condition)) +
  geom_point(position = position_jitter(w = 0.1, h = 0), size = 5) +
  scale_color_manual(values=c("#0000FF", "#FF8000", "#AD07E3")) +
  theme_bw() +
  xlab("Condition")+
  ylab("Normalized Counts")+
  ggtitle(
    label = "Setdb1 Expression",
    subtitle = "Normalized Gene Expression"
  )

a

Past versions of "Selected Genes5-1.png"

Version	Author	Date
a1c090c	avm27	2024-07-17
dc04b15	avm27	2024-07-17

5.1.6 Atf7ip

#### Atf7ip

d2 <- plotCounts(dds,
  gene = "Atf7ip|Atf7ip", intgroup = "condition",
  returnData = TRUE
)

a <- ggplot(d2, aes(x = factor(condition, level = level_order), y = count, color = condition)) +
  geom_point(position = position_jitter(w = 0.1, h = 0), size = 5) +
  scale_color_manual(values=c("#0000FF", "#FF8000", "#AD07E3")) +
  theme_bw() +
  xlab("Condition")+
  ylab("Normalized Counts")+
  ggtitle(
    label = "Atf7ip Expression",
    subtitle = "Normalized Gene Expression"
  )

a

Past versions of "Selected Genes6-1.png"

Version	Author	Date
a1c090c	avm27	2024-07-17
dc04b15	avm27	2024-07-17

5.2 Principal Components Analysis (PCA)

For visualization I am converting all analyses to logarithmic. Following this I have completed a PCA for each analyses based on all genes together.

Past versions of "Plot PCA-1.png"

Version	Author	Date
a1c090c	avm27	2024-07-17
dc04b15	avm27	2024-07-17

5.3 Venn Diagrams

5.3.1 Up-Regulated Genes

myCol <- brewer.pal(3, "Pastel2")

results_sig_Table_up <- subset(results_sig, log2FoldChange > 0)
results_sig2_Table_up <- subset(results_sig2, log2FoldChange > 0)
results_sig3_Table_up <- subset(results_sig3, log2FoldChange > 0)

new_ressig1_up  <- rownames(results_sig_Table_up)
new_ressig2_up <- rownames(results_sig2_Table_up)
new_ressig3_up  <- rownames(results_sig3_Table_up)

# Generate Venn Diagram 
venn.plot.up <- venn.diagram(
  x = list(
    "Crv_vs_FT" = new_ressig1_up,
    "Maint_vs_FT" = new_ressig2_up,
    "Crv_vs_Maint" = new_ressig3_up),
    fill = myCol,
    cex = .8,
    fontface = "bold",
    fontfamily = "sans",
    cat.cex = 0.8,
    cat.fontface = "bold",
    cat.default.pos = "outer",
    cat.pos = c(0, 0, 0),
    cat.fontfamily = "sans",
    rotation = 1,
  category.names = c("Craving_vs_FoodTrained", "Maintenance_vs_FoodTrained", "Craving_vs_Maintenance"),
  filename = NULL,
  output = TRUE
)

# Save Venn Diagram
#pdf("plots/CIVSA_venn_diagram_Up.pdf")
grid.draw(venn.plot.up)

Past versions of unnamed-chunk-1-1.png

Version	Author	Date
dc04b15	avm27	2024-07-17

#dev.off()

# Display Venn Diagram in RStudio
#grid.draw(venn.plot.up)

5.3.2 Down-Regulated Genes

results_sig_Table_down <- subset(results_sig, log2FoldChange < 0)
results_sig2_Table_down <- subset(results_sig2, log2FoldChange < 0)
results_sig3_Table_down <- subset(results_sig3, log2FoldChange < 0)

new_ressig1_down  <- rownames(results_sig_Table_down)
new_ressig2_down  <- rownames(results_sig2_Table_down)
new_ressig3_down  <- rownames(results_sig3_Table_down)


# Generate Venn Diagram UP
venn.plot.down <- venn.diagram(
  x = list(
    "Crv_vs_FT" = new_ressig1_down,
    "Maint_vs_FT" = new_ressig2_down,
    "Crv_vs_Maint" = new_ressig3_down),
    fill = myCol,
    cex = .8,
    fontface = "bold",
    fontfamily = "sans",
    cat.cex = 0.8,
    cat.fontface = "bold",
    cat.default.pos = "outer",
    cat.pos = c(0, 0, 0),
    cat.fontfamily = "sans",
    rotation = 1,
  category.names = c("Craving_vs_FoodTrained", "Maintenance_vs_FoodTrained", "Craving_vs_Maintenance"),
  filename = NULL,
  output = TRUE
)

# Save Venn Diagram
#pdf("plots/CIVSA_venn_diagram_Down.pdf")
#grid.draw(venn.plot.down)
#dev.off()

# Display Venn Diagram in RStudio
grid.draw(venn.plot.down)

Past versions of unnamed-chunk-2-1.png

Version	Author	Date
dc04b15	avm27	2024-07-17

5.4 Heatmaps of Differentially Expressed Genes

ressig1 <- as.data.frame(results_sig)
ressig2 <- as.data.frame(results_sig2)
ressig3 <- as.data.frame(results_sig3)

ressig1$Comparison <- "Craving vs FoodTrained"
ressig2$Comparison <- "Maintenance vs FoodTrained"
ressig3$Comparison <- "Craving vs Maintenance"

ressig1_highlfc_pos <- ressig1[ressig1$log2FoldChange >= 1.5,]
ressig1_highlfc_neg <- ressig1[ressig1$log2FoldChange <= -1.5,]
ressig2_highlfc_pos <- ressig2[ressig2$log2FoldChange >= 1.5,]
ressig2_highlfc_neg <- ressig2[ressig2$log2FoldChange <= -1.5,]
ressig3_highlfc_pos <- ressig3[ressig3$log2FoldChange >= 1.5,]
ressig3_highlfc_neg <- ressig3[ressig3$log2FoldChange <= -1.5,]

temp_sigdegshm <- rbind(ressig1_highlfc_pos, ressig1_highlfc_neg)
temp_sigdegshm2 <- rbind(temp_sigdegshm, ressig2_highlfc_pos)
temp_sigdegshm3 <- rbind(temp_sigdegshm2, ressig2_highlfc_neg)
temp_sigdegshm4 <- rbind(temp_sigdegshm3, ressig3_highlfc_pos)
temp_sigdegshm5 <- rbind(temp_sigdegshm4, ressig3_highlfc_neg)

temp_sigdegshm6 <- temp_sigdegshm5[temp_sigdegshm5$lfcSE <=1,]

dup_rows <- duplicated(temp_sigdegshm6$symbol)
data_dedup <- temp_sigdegshm6[!dup_rows, ]

rows <- rownames(data_dedup)

select <- order(rowMeans(counts(dds,normalized=TRUE)),
                decreasing=TRUE)#[1:1500]

mat <- assay(ddsMat_rlog)[select,]

data_mod <- mat[rownames(mat) %in% rows, ] 

matrownames_data_mod <- data.frame(rownames(data_mod))

matrownames_data_mod <- matrownames_data_mod %>% separate(rownames.data_mod., c("id", "symbol"),sep ="([|])")

samples <- as.tibble(read.csv("data/sample_info_CIVSA.csv", sep = ","))

annot_col <- samples %>%
  column_to_rownames('samplename') %>%
  as.data.frame()

ann_colors = list(
  condition = as.factor(c(FoodTrained = "#0000FF", Maintenance = "#AD07E3", Craving = "#FF8000")),
  Group = as.factor(c(FoodTrained = "#0000FF", Maintenance = "#AD07E3", Craving = "#FF8000")))

5.4.1 Unsupervised Clustering

pheatmap::pheatmap(
  mat = data_mod,
  color = colorRampPalette(rev(brewer.pal(11, "RdYlBu")))(155),
  scale = "row",
  annotation_colors = ann_colors,
  annotation_col = annot_col,
  fontsize = 10, 
  show_colnames = T,
  cluster_rows = T,
  cluster_cols = T,
  annotation_legend = T,
  legend = T,
  show_rownames = F,
  clustering_distance_rows = "correlation",
  clustering_method = "ward.D",
  main = "Heatmap of Significant DEGs -- Unsupervised Clustering",
  cluster_row_slices = TRUE,
  show_row_dend = FALSE,
  cutree_rows = 4,
  cutree_cols = 3,
  treeheight_row = 10,
  treeheight_col = 10,
  legend_labels = c("FoodTrained", "Maintenance", "Craving")
)

Past versions of "Filter Heatmaps by DEGs2 Unsupervised-1.png"

Version	Author	Date
a1c090c	avm27	2024-07-17
dc04b15	avm27	2024-07-17

5.4.2 Supervised Clustering

pheatmap::pheatmap(
  mat = data_mod,
  color = colorRampPalette(rev(brewer.pal(11, "RdYlBu")))(155),
  scale = "row",
  annotation_col = annot_col,
  annotation_colors = ann_colors,
  fontsize = 10,
  show_colnames = T,
  cluster_rows = T,
  cluster_cols = F,
  annotation_legend = T,
  legend = T,
  show_rownames = F,
  clustering_distance_rows = "correlation",
  clustering_method = "ward.D",
  main = "Heatmap of Significant DEGs -- Supervised Clustering",
  cluster_row_slices = TRUE,
  show_row_dend = FALSE,
  cutree_rows = 4,
  cutree_cols = 3,
  gaps_col = c(3, 6),
  treeheight_row = 10,
  treeheight_col = 10,
  legend_labels = c("FoodTrained", "Maintenance", "Craving"),
)

Past versions of "Filter Heatmaps by DEGs2 Condensed-Supervised-1.png"

Version	Author	Date
a1c090c	avm27	2024-07-17
dc04b15	avm27	2024-07-17

5.5 Volcano Plots

5.5.1 Visualize Results: Volcano Plots (Non-Interactive)

Volcano plots are generated by gathering the FDR corrected p-values from each analysis. The adjusted p-values undergo a -log10 transformation to generate these FDR corrected values. Any rows containing “NA” are ommitted from analysis. Data points are colored based on increasing or decreasing value and plotted using ggplot2. Adjusted p-value cutoff is 1.3 following log transformation.(-log10 0.05 = 1.3)

                               baseMean log2FoldChange     lfcSE      stat
Gm28836|Gm28836                24.57062     18.5128950 3.6825760  5.027159
Vwa3b|Vwa3b                    68.09876      9.3220787 2.2726944  4.101774
4930439A04Rik|4930439A04Rik   239.71050      6.0863907 1.0543294  5.772760
LOC108167622|LOC108167622      55.54376     21.2716434 2.7752955  7.664641
Pard3bos2|Pard3bos2            48.12983    -22.8631637 3.6323379 -6.294338
Col4a3|Col4a3                  29.96706     19.6012026 3.5629545  5.501390
Dnajb3|Dnajb3                  70.36681      9.0935226 2.0877638  4.355628
Asb18|Asb18                    12.85015     18.8221148 3.6835623  5.109759
Gm41920|Gm41920                91.39199     20.7669259 3.6195797  5.737386
LOC105246710|LOC105246710      41.29964     21.3720390 3.6789651  5.809253
LOC108167732|LOC108167732      59.78860     21.9826855 3.2366754  6.791749
Fam129a|Fam129a                58.26340      9.5420991 2.6179113  3.644928
Fmo1|Fmo1                      51.26689     21.6153849 2.7780474  7.780783
Gorab|Gorab                   666.84329      2.7745936 0.5327144  5.208407
Dnah14|Dnah14                  41.60299     21.3346812 3.4180513  6.241767
Atf3|Atf3                     433.56152     -2.8083301 0.7372279 -3.809311
B230208H11Rik|B230208H11Rik    48.28040     21.7619394 2.7106546  8.028297
LOC108167797|LOC108167797      82.55280      9.4565102 2.0988898  4.505482
Fam26f|Fam26f                  45.72461     21.0352860 2.7780345  7.572003
Mical1|Mical1                 109.45019     10.5854874 2.6621850  3.976240
LOC108167812|LOC108167812      48.48680     21.0367818 3.3422862  6.294129
Upb1|Upb1                      31.15323     20.8834313 2.8559936  7.312142
Eid3|Eid3                      49.98683     20.3594803 3.5216112  5.781297
Gm5174|Gm5174                 159.96921      9.8691990 1.6538122  5.967545
Gm32898|Gm32898               117.28305     22.8672302 3.6150540  6.325557
5730420D15Rik|5730420D15Rik    43.60017      8.4963808 2.1885102  3.882267
Nab2|Nab2                      75.41202     10.0480657 2.8971733  3.468231
Itga7|Itga7                   381.36001      1.6274389 0.4495805  3.619906
Pkd1l1|Pkd1l1                  38.79214     20.9493623 3.4199995  6.125545
Hba-a1|Hba-a1                6141.73399     -1.5647899 0.3769493 -4.151194
Hba-a2|Hba-a2                3472.37285     -1.5623216 0.3798307 -4.113205
Maml1|Maml1                   233.34793      5.0920190 1.3477327  3.778211
Zfp354a|Zfp354a               852.34344      2.1089012 0.5552005  3.798450
Pemt|Pemt                     152.14561      2.5555017 0.7365142  3.469725
F930015N05Rik|F930015N05Rik    55.86007      9.6148803 2.1140499  4.548086
Nxn|Nxn                       319.92588     -1.9620641 0.3778538 -5.192654
Gm29979|Gm29979                13.99564     19.0280261 3.6827924  5.166739
Mmp28|Mmp28                    27.63828     20.4282683 3.6798100  5.551446
Hnf1b|Hnf1b                    22.98457     19.0698503 3.6825965  5.178371
Gm525|Gm525                    35.40808     19.2788261 3.6818171  5.236226
Rara|Rara                     124.45357     10.4694702 1.8818981  5.563250
Zfp385c|Zfp385c                47.59639     21.2456232 3.6790363  5.774779
Aoc2|Aoc2                     119.08053     10.1859549 2.1874916  4.656454
Brca1|Brca1                    33.72022     20.9199760 3.4207695  6.115576
Sphk1|Sphk1                   432.30661      2.9324030 0.6969297  4.207602
Gen1|Gen1                      55.25217      9.3302818 2.3993645  3.888647
Prps1l3|Prps1l3              1462.49697     -1.5781279 0.4468833 -3.531410
Gm20337|Gm20337               101.79198      9.8406189 1.7844311  5.514709
Gm38543|Gm38543                25.84064     19.9627304 3.6726977  5.435441
Gm33682|Gm33682                20.71715     19.3033678 3.6819210  5.242744
AW209491|AW209491            5340.94808     -0.8402446 0.2242000 -3.747746
Hus1b|Hus1b                    26.74186     20.6087597 3.6796147  5.600793
A230103O09Rik|A230103O09Rik    13.02921     18.5256807 3.6848214  5.027565
Gm31683|Gm31683                50.38814     19.9794226 3.6803986  5.428603
Catsper3|Catsper3              47.43489     20.9338126 2.7864181  7.512804
1810034E14Rik|1810034E14Rik    31.92691      8.8079724 2.4165323  3.644881
Exoc3|Exoc3                  3834.74743      0.6112165 0.1637856  3.731808
Gm38604|Gm38604                29.19617     20.6125065 3.6019627  5.722576
3110070M22Rik|3110070M22Rik    60.66760      8.2325711 2.3336607  3.527750
Mmrn2|Mmrn2                   180.80825      9.9276820 1.5025893  6.607049
Cdhr1|Cdhr1                    63.78466      9.3100733 2.2586018  4.122052
4930563I02Rik|4930563I02Rik    36.90587     22.4601329 3.6787584  6.105357
Arl11|Arl11                    41.95117     20.9422958 3.6792700  5.691970
Gm35679|Gm35679                25.36328     20.6484297 3.6795756  5.611634
Samd12|Samd12                1758.47866     -0.8719704 0.2526747 -3.450961
Col22a1|Col22a1                46.34553      9.2068937 2.5613267  3.594580
Gm44502|Gm44502               309.78321      5.3844138 1.2858520  4.187429
A330009N23Rik|A330009N23Rik    55.82716      9.4892318 2.6212576  3.620107
Gm16861|Gm16861                23.45444      5.8057233 1.6448169  3.529708
Eef2kmt|Eef2kmt                95.32773      9.3145556 2.2868530  4.073089
Sdf2l1|Sdf2l1                5369.91374     -0.8036952 0.2287679 -3.513146
Lrrc74b|Lrrc74b                39.81330     21.4504268 3.6788989  5.830665
Tfrc|Tfrc                    7210.69143      1.2224025 0.2745212  4.452852
Dopey2|Dopey2                1489.53289      0.8594281 0.2136690  4.022240
Gm41523|Gm41523                29.93678     20.8161452 3.4818066  5.978547
Mas1|Mas1                     163.03444      9.6805312 2.4765306  3.908908
Tbl3|Tbl3                    2380.06543      0.8426457 0.2439577  3.454065
Tead3|Tead3                    37.05380      9.0228667 2.3736949  3.801191
Cdkn1a|Cdkn1a                 609.20590     -2.0366912 0.5167820 -3.941103
Hsf2bp|Hsf2bp                  85.34559     21.5755849 3.6788213  5.864809
Zfp811|Zfp811                 514.60028      1.6438065 0.3782180  4.346188
H2-K1|H2-K1                  2113.14570     -1.7493922 0.4407086 -3.969499
H2-DMa|H2-DMa                1379.29871     -1.0932894 0.3167851 -3.451202
Nfkbie|Nfkbie                  55.75806      9.5621184 2.2965492  4.163690
Ebi3|Ebi3                      69.18583      9.5361302 2.1756271  4.383164
Crb3|Crb3                     157.64220      5.4059294 1.3183645  4.100482
Hnrnpll|Hnrnpll              1439.23224      1.0138761 0.2872519  3.529572
4930543D07Rik|4930543D07Rik    26.85209     20.0710513 3.6716893  5.466435
Ttr|Ttr                        49.47335     21.6246440 2.6997135  8.009977
BC051408|BC051408              52.13171     20.6191470 3.6795567  5.603704
Apbb3|Apbb3                  2349.96752      1.1291084 0.2519717  4.481092
Dnd1|Dnd1                      50.74157      9.2508675 2.6424046  3.500928
Tex43|Tex43                    27.24572     20.7268208 3.5795879  5.790281
Gm41795|Gm41795                28.87951      6.9506762 1.8445941  3.768133
Ptgdr2|Ptgdr2                  56.55581    -23.8987364 3.6250264 -6.592707
LOC108168412|LOC108168412     624.56923     -1.9670535 0.4438242 -4.432055
Gm30990|Gm30990                33.69945     20.9416614 3.5266620  5.938097
Ablim1|Ablim1                3587.79642      0.9295199 0.2688121  3.457880
LOC108168424|LOC108168424     183.91856      6.4961023 1.2774999  5.085012
Gm33534|Gm33534                29.75061     20.9387040 3.6792957  5.690954
Rnd3|Rnd3                     665.74838      1.8164903 0.5010974  3.625024
Ppp1r1c|Ppp1r1c                29.28284     20.8577755 2.9018057  7.187861
Slc43a3|Slc43a3                55.81427     19.3109284 3.6817910  5.244982
Actc1|Actc1                    18.82778     19.4617722 3.6815354  5.286319
LOC108168839|LOC108168839     319.10738      1.4552344 0.3952092  3.682188
1810024B03Rik|1810024B03Rik    26.08745      8.0069112 2.0817535  3.846234
Oxt|Oxt                        41.16708     19.9234500 3.6805016  5.413243
Gm33648|Gm33648                52.87639     21.0777793 3.6791487  5.728983
Cfap61|Cfap61                  16.85763     19.6207507 3.1709108  6.187733
Rprd1b|Rprd1b                1254.90512      1.2500708 0.3004688  4.160401
Npepl1|Npepl1                 153.75375      6.6264373 1.7046540  3.887262
Fgf2|Fgf2                      17.28854     19.7961355 3.6808183  5.378189
Ctso|Ctso                    1640.84353     -0.9540699 0.2545610 -3.747903
Gm30352|Gm30352                53.94418     20.8499756 3.6793342  5.666780
Ash1l|Ash1l                 14133.38248     -0.6288111 0.1796736 -3.499740
Rorc|Rorc                      47.34537      9.2652269 2.0869583  4.439584
Snx27|Snx27                  4561.14782      0.8052498 0.2269326  3.548410
Setdb1|Setdb1                1078.28097      1.8332332 0.4059185  4.516259
Hist2h4|Hist2h4               261.68889     -2.2456967 0.6506238 -3.451606
LOC108168896|LOC108168896      36.52730      9.0020265 2.4052657  3.742633
Gm35408|Gm35408                68.99380     20.5071858 3.6796604  5.573119
LOC108168900|LOC108168900      66.03254      8.9847600 2.1738101  4.133185
Gm40150|Gm40150                54.70566     21.3424611 2.8807120  7.408745
Emcn|Emcn                      41.35474     21.5910128 3.3183283  6.506593
Gm40187|Gm40187                27.43375     20.0081770 3.6804027  5.436410
Ube2r2|Ube2r2                 841.04416      1.3034045 0.3199099  4.074286
Gm38592|Gm38592              4519.05552     -0.8064118 0.2293080 -3.516719
Tusc1|Tusc1                    98.86480      8.3250368 1.8670482  4.458930
Cyp2j12|Cyp2j12                89.53863      9.5148586 2.1776588  4.369307
Gm12701|Gm12701                53.33441     21.6897447 3.2584153  6.656532
Mroh7|Mroh7                    82.94129      8.8298603 2.1825628  4.045639
LOC102634683|LOC102634683      19.06256     19.4210096 3.6816289  5.275113
Ccdc27|Ccdc27                  29.90957      7.0653729 1.9560315  3.612096
Gm42362|Gm42362                16.33002     19.3085795 3.6819273  5.244150
Plekhn1|Plekhn1               128.52306      9.1673339 2.5844520  3.547109
Gm29868|Gm29868                50.31169     20.4473368 3.4270082  5.966527
Gm5106|Gm5106                  37.86683     21.4530851 2.7097316  7.917052
Crot|Crot                    2514.09062      1.0696344 0.2200188  4.861559
Gm15421|Gm15421               113.25793      3.4337909 0.9432909  3.640225
Gm35055|Gm35055                63.03573      6.9221102 1.8903776  3.661761
Gm15614|Gm15614                90.50337      9.4491834 2.1391512  4.417258
Evc|Evc                       188.57980      4.5076075 1.1288645  3.993046
Lyar|Lyar                     356.46936      5.0874798 0.9854807  5.162435
Gm40291|Gm40291                25.68616     20.6763711 2.9116040  7.101368
Gm35394|Gm35394                84.93855     22.6300121 3.0745731  7.360375
Asphd2|Asphd2                2738.83643     -0.8550400 0.1989029 -4.298780
4930515G01Rik|4930515G01Rik    26.98503     20.3062006 3.5593961  5.704957
Ccdc64|Ccdc64                 851.59146      1.2876173 0.2968491  4.337615
Fzd10|Fzd10                    76.52292      8.2419992 2.3930853  3.444089
A330070K13Rik|A330070K13Rik    25.10801      7.3684430 1.7839359  4.130442
Pilra|Pilra                    41.24013      9.1773331 2.2027436  4.166319
Pds5b|Pds5b                  2200.85686      0.6254481 0.1485377  4.210704
Pole4|Pole4                   628.28581      1.6959280 0.3492780  4.855525
5031434C07Rik|5031434C07Rik    27.10674     20.5005598 3.6797258  5.571219
Gm38876|Gm38876                52.15738     20.9819471 3.6792271  5.702814
Mug2|Mug2                      65.40982      9.7120836 2.4931589  3.895493
Gm33449|Gm33449                63.41728     21.6643816 3.3222338  6.521029
Olr1|Olr1                      21.67954     20.2830410 3.6799834  5.511721
Plbd1|Plbd1                    26.07896     20.4133820 2.9786727  6.853181
Ehd2|Ehd2                      76.96763     10.0775311 2.8416275  3.546394
Ccdc9|Ccdc9                   265.00133     -2.3279801 0.6734146 -3.456979
Ceacam2|Ceacam2                41.25384      8.5233352 2.2190907  3.840913
Zfp607|Zfp607                  69.25108     20.4514697 3.6797281  5.557875
Map4k1|Map4k1                 197.36808     11.1844124 1.8881700  5.923414
Kctd15|Kctd15                  95.98999      5.9499460 1.2365348  4.811790
Il4i1|Il4i1                    52.53011      9.5263849 2.2156960  4.299500
Kctd14|Kctd14                  36.38576     20.5606991 3.6796361  5.587699
Hbb-bt|Hbb-bt                 791.65194     -2.0146527 0.5513906 -3.653767
Hbb-bs|Hbb-bs                7534.89488     -1.7587126 0.4009505 -4.386358
Tpcn2|Tpcn2                   143.98364     10.3454565 1.7388133  5.949722
Ints10|Ints10                4134.33556      0.7041970 0.1969123  3.576196
Bst2|Bst2                     420.49605     -2.2772975 0.5541767 -4.109334
Klf1|Klf1                      48.00653     20.3865370 3.3466670  6.091594
2310036O22Rik|2310036O22Rik   570.95340      1.8732520 0.4342911  4.313356
Gm32122|Gm32122                31.11654      8.7470506 2.3774133  3.679230
Fhod1|Fhod1                    61.21780      8.2780398 2.3404712  3.536912
Ctcf|Ctcf                    1114.10791      1.1231348 0.2740135  4.098830
Calb2|Calb2                  5122.62050     -0.9092178 0.2185685 -4.159876
LOC108167554|LOC108167554      65.48991     21.0213989 3.6791843  5.713603
Osgin1|Osgin1                  51.29313     21.2055438 2.7939138  7.589906
Vps9d1|Vps9d1                1212.61307      0.8840355 0.2202258  4.014223
Oaf|Oaf                        43.18681     20.4213091 2.8198247  7.242049
Ccdc153|Ccdc153                23.62259     20.3302930 3.6799468  5.524616
Stra6|Stra6                    78.82205     22.6054518 3.0754392  7.350317
Gm39386|Gm39386                25.84677     20.1785647 3.6801437  5.483091
D030055H07Rik|D030055H07Rik    40.38475      8.2584874 2.2519530  3.667256
Manf|Manf                    6703.22186     -0.6778414 0.1844009 -3.675912
Traip|Traip                    76.72515      9.0919295 2.2661959  4.011979
Gm38623|Gm38623                30.77395      8.7546935 2.4878635  3.518961
Ubp1|Ubp1                    1929.70430      1.4223916 0.4137043  3.438184
Cul4b|Cul4b                   884.20012      1.7414287 0.4512856  3.858818
Stk26|Stk26                    51.21756     21.4394753 2.7794753  7.713497
4930502E18Rik|4930502E18Rik    62.74241      9.2126859 2.4446391  3.768526
4933403O08Rik|4933403O08Rik    34.01902     20.7907256 3.4787527  5.976489
Nms|Nms                       118.00946     21.7264330 3.0521191  7.118475
Gm30900|Gm30900                15.50308     19.3612076 3.6818032  5.258621
Gm41939|Gm41939                22.02437    -21.3109700 3.6360149 -5.861079
Lamc2|Lamc2                   168.34710     21.8441186 2.9959647  7.291180
4930523C07Rik|4930523C07Rik    55.69843     21.6016786 3.6788171  5.871909
Gm32749|Gm32749                14.86627     20.2053938 3.6801544  5.490366
Gm33377|Gm33377                29.87861     19.5017422 3.6813760  5.297406
Efemp1|Efemp1                 145.24603      9.6484478 2.0729282  4.654502
Wnt9a|Wnt9a                    20.87398     19.2242250 3.6821382  5.220941
Cldn7|Cldn7                    33.89146     20.5899973 3.4664368  5.939816
Rhbdf2|Rhbdf2                  62.95520     21.9131521 3.2057205  6.835640
LOC108167980|LOC108167980      20.26089     19.8659910 3.6806693  5.397385
Gm34489|Gm34489                32.14988    -22.9371198 3.6322479 -6.314855
Gm40375|Gm40375                11.71586     19.3048148 3.6820147  5.243003
Gm40474|Gm40474               116.78933      8.9256675 2.5453467  3.506661
Gm5086|Gm5086                  64.68465     19.7334045 3.6808184  5.361146
Gm31452|Gm31452                22.17355     19.4799358 3.6814597  5.291362
Gm30363|Gm30363                26.34376     20.1908566 3.6801222  5.486464
Il17rd|Il17rd                  93.82029      9.7292810 2.6262307  3.704656
Mir17hg|Mir17hg                28.31683     19.3173112 3.6818444  5.246640
Capsl|Capsl                    30.37335     19.8103917 3.5318311  5.609099
Gm41447|Gm41447                18.48080     19.6241531 3.6807334  5.331588
Drd3|Drd3                      44.70458     21.6519209 3.2837107  6.593736
Rsph1|Rsph1                    31.39588     20.9862862 3.5299440  5.945218
Gpsm3|Gpsm3                    66.44566      9.4598589 2.6294987  3.597590
Slc22a7|Slc22a7                34.67828     18.8182113 3.6830811  5.109367
Plin5|Plin5                    41.95955     20.9819788 3.6788744  5.703369
Tbc1d10c|Tbc1d10c              30.12516     20.6333658 3.5565825  5.801459
Olfr1417|Olfr1417              13.19659     17.4401304 3.6925777  4.723023
Fut7|Fut7                      26.31352     20.7112535 3.6795087  5.628809
Dbh|Dbh                        50.67095     22.6647496 3.6785735  6.161288
Spc25|Spc25                    27.40374    -22.2493370 3.6333059 -6.123717
4833423E24Rik|4833423E24Rik    56.49302    -22.8630913 3.6323015 -6.294381
Rad51|Rad51                    48.65376     21.9659958 3.6786622  5.971191
Cd40|Cd40                      59.94672     20.5992944 3.6795590  5.598305
Gm39990|Gm39990                17.35011     19.4432986 3.6815834  5.281233
Helz2|Helz2                    37.23905     19.3008354 3.6818613  5.242141
Sprr1a|Sprr1a                  41.70288    -23.5330453 3.0814495 -7.637005
Hist2h2bb|Hist2h2bb            15.66563     19.4297337 3.6816221  5.277493
Gabrr1|Gabrr1                  54.60723     20.7392352 3.6794252  5.636542
Hspb7|Hspb7                    23.79337     20.4817819 3.6797636  5.566059
Gm32374|Gm32374                21.12432    -20.5479366 3.6401222 -5.644848
Gm40349|Gm40349                25.78198     20.4998113 3.6796825  5.571082
Vmn1r4|Vmn1r4                  37.07423     20.2410236 3.6800265  5.500238
Mcm2|Mcm2                      90.46134      9.2284770 2.6558569  3.474764
Lpar5|Lpar5                    85.89744    -23.1936451 3.4069875 -6.807670
Zfp541|Zfp541                  37.85256      8.0665338 2.2516092  3.582564
Rcn3|Rcn3                      47.96203     21.0339348 3.6791881  5.717004
LOC108167437|LOC108167437     158.80359      8.8401015 2.5735323  3.435007
Gm35021|Gm35021                17.35979     19.1839768 3.6822477  5.209855
Ces5a|Ces5a                    35.44598     20.5447286 3.6796552  5.583330
Il10ra|Il10ra                  34.19337     21.0615824 3.5476436  5.936781
Gm15169|Gm15169               112.48380     21.5540737 3.5946365  5.996176
                                  pvalue         padj        symbol
Gm28836|Gm28836             4.977997e-07 7.484695e-05       Gm28836
Vwa3b|Vwa3b                 4.099948e-05 4.809591e-03         Vwa3b
4930439A04Rik|4930439A04Rik 7.798346e-09 2.473294e-06 4930439A04Rik
LOC108167622|LOC108167622   1.793321e-14 6.066804e-11  LOC108167622
Pard3bos2|Pard3bos2         3.087138e-10 1.845506e-07     Pard3bos2
Col4a3|Col4a3               3.768086e-08 7.936683e-06        Col4a3
Dnajb3|Dnajb3               1.326860e-05 1.748870e-03        Dnajb3
Asb18|Asb18                 3.225705e-07 4.970561e-05         Asb18
Gm41920|Gm41920             9.614896e-09 3.002510e-06       Gm41920
LOC105246710|LOC105246710   6.275220e-09 2.158889e-06  LOC105246710
LOC108167732|LOC108167732   1.107824e-11 9.776791e-09  LOC108167732
Fam129a|Fam129a             2.674662e-04 2.561336e-02       Fam129a
Fmo1|Fmo1                   7.207684e-15 3.657539e-11          Fmo1
Gorab|Gorab                 1.904688e-07 3.068362e-05         Gorab
Dnah14|Dnah14               4.326538e-10 2.509145e-07        Dnah14
Atf3|Atf3                   1.393547e-04 1.458053e-02          Atf3
B230208H11Rik|B230208H11Rik 9.883523e-16 1.164391e-11 B230208H11Rik
LOC108167797|LOC108167797   6.622245e-06 9.334606e-04  LOC108167797
Fam26f|Fam26f               3.675124e-14 8.288630e-11        Fam26f
Mical1|Mical1               7.001335e-05 7.765744e-03        Mical1
LOC108167812|LOC108167812   3.091300e-10 1.845506e-07  LOC108167812
Upb1|Upb1                   2.629167e-13 3.811916e-10          Upb1
Eid3|Eid3                   7.412691e-09 2.426819e-06          Eid3
Gm5174|Gm5174               2.408498e-09 1.024866e-06        Gm5174
Gm32898|Gm32898             2.523206e-10 1.707201e-07       Gm32898
5730420D15Rik|5730420D15Rik 1.034872e-04 1.105570e-02 5730420D15Rik
Nab2|Nab2                   5.238972e-04 4.468095e-02          Nab2
Itga7|Itga7                 2.947106e-04 2.769461e-02         Itga7
Pkd1l1|Pkd1l1               9.037347e-10 4.757914e-07        Pkd1l1
Hba-a1|Hba-a1               3.307448e-05 4.020035e-03        Hba-a1
Hba-a2|Hba-a2               3.902034e-05 4.631783e-03        Hba-a2
Maml1|Maml1                 1.579589e-04 1.627538e-02         Maml1
Zfp354a|Zfp354a             1.456041e-04 1.507894e-02       Zfp354a
Pemt|Pemt                   5.209916e-04 4.462062e-02          Pemt
F930015N05Rik|F930015N05Rik 5.413606e-06 7.738406e-04 F930015N05Rik
Nxn|Nxn                     2.073171e-07 3.313482e-05           Nxn
Gm29979|Gm29979             2.382138e-07 3.748267e-05       Gm29979
Mmp28|Mmp28                 2.833155e-08 6.250803e-06         Mmp28
Hnf1b|Hnf1b                 2.238319e-07 3.549484e-05         Hnf1b
Gm525|Gm525                 1.638933e-07 2.704640e-05         Gm525
Rara|Rara                   2.647957e-08 5.972026e-06          Rara
Zfp385c|Zfp385c             7.705398e-09 2.473294e-06       Zfp385c
Aoc2|Aoc2                   3.217013e-06 4.664210e-04          Aoc2
Brca1|Brca1                 9.620876e-10 4.882114e-07         Brca1
Sphk1|Sphk1                 2.580947e-05 3.253917e-03         Sphk1
Gen1|Gen1                   1.008046e-04 1.088368e-02          Gen1
Prps1l3|Prps1l3             4.133509e-04 3.705566e-02       Prps1l3
Gm20337|Gm20337             3.493566e-08 7.543872e-06       Gm20337
Gm38543|Gm38543             5.466118e-08 1.077197e-05       Gm38543
Gm33682|Gm33682             1.582063e-07 2.640805e-05       Gm33682
AW209491|AW209491           1.784311e-04 1.801888e-02      AW209491
Hus1b|Hus1b                 2.133735e-08 5.281775e-06         Hus1b
A230103O09Rik|A230103O09Rik 4.967460e-07 7.484695e-05 A230103O09Rik
Gm31683|Gm31683             5.679687e-08 1.108522e-05       Gm31683
Catsper3|Catsper3           5.787421e-14 1.174731e-10      Catsper3
1810034E14Rik|1810034E14Rik 2.675156e-04 2.561336e-02 1810034E14Rik
Exoc3|Exoc3                 1.901104e-04 1.900917e-02         Exoc3
Gm38604|Gm38604             1.049207e-08 3.178627e-06       Gm38604
3110070M22Rik|3110070M22Rik 4.191082e-04 3.714872e-02 3110070M22Rik
Mmrn2|Mmrn2                 3.920550e-11 3.183173e-08         Mmrn2
Cdhr1|Cdhr1                 3.755129e-05 4.483624e-03         Cdhr1
4930563I02Rik|4930563I02Rik 1.025712e-09 5.078027e-07 4930563I02Rik
Arl11|Arl11                 1.255816e-08 3.465232e-06         Arl11
Gm35679|Gm35679             2.004256e-08 5.149669e-06       Gm35679
Samd12|Samd12               5.585952e-04 4.646871e-02        Samd12
Col22a1|Col22a1             3.249154e-04 3.011476e-02       Col22a1
Gm44502|Gm44502             2.821322e-05 3.535012e-03       Gm44502
A330009N23Rik|A330009N23Rik 2.944817e-04 2.769461e-02 A330009N23Rik
Gm16861|Gm16861             4.160186e-04 3.705566e-02       Gm16861
Eef2kmt|Eef2kmt             4.639369e-05 5.320334e-03       Eef2kmt
Sdf2l1|Sdf2l1               4.428343e-04 3.874418e-02        Sdf2l1
Lrrc74b|Lrrc74b             5.520697e-09 1.932053e-06       Lrrc74b
Tfrc|Tfrc                   8.473718e-06 1.170065e-03          Tfrc
Dopey2|Dopey2               5.764729e-05 6.537009e-03        Dopey2
Gm41523|Gm41523             2.251363e-09 1.024866e-06       Gm41523
Mas1|Mas1                   9.271410e-05 1.011780e-02          Mas1
Tbl3|Tbl3                   5.522037e-04 4.646871e-02          Tbl3
Tead3|Tead3                 1.440024e-04 1.498955e-02         Tead3
Cdkn1a|Cdkn1a               8.110782e-05 8.899063e-03        Cdkn1a
Hsf2bp|Hsf2bp               4.496495e-09 1.629819e-06        Hsf2bp
Zfp811|Zfp811               1.385238e-05 1.814037e-03        Zfp811
H2-K1|H2-K1                 7.202392e-05 7.945335e-03         H2-K1
H2-DMa|H2-DMa               5.580962e-04 4.646871e-02        H2-DMa
Nfkbie|Nfkbie               3.131455e-05 3.875748e-03        Nfkbie
Ebi3|Ebi3                   1.169681e-05 1.561985e-03          Ebi3
Crb3|Crb3                   4.122913e-05 4.809591e-03          Crb3
Hnrnpll|Hnrnpll             4.162326e-04 3.705566e-02       Hnrnpll
4930543D07Rik|4930543D07Rik 4.591765e-08 9.228083e-06 4930543D07Rik
Ttr|Ttr                     1.147297e-15 1.164391e-11           Ttr
BC051408|BC051408           2.098188e-08 5.257904e-06      BC051408
Apbb3|Apbb3                 7.426204e-06 1.039566e-03         Apbb3
Dnd1|Dnd1                   4.636416e-04 4.021794e-02          Dnd1
Tex43|Tex43                 7.026867e-09 2.338219e-06         Tex43
Gm41795|Gm41795             1.644730e-04 1.677624e-02       Gm41795
Ptgdr2|Ptgdr2               4.318790e-11 3.246771e-08        Ptgdr2
LOC108168412|LOC108168412   9.333913e-06 1.271542e-03  LOC108168412
Gm30990|Gm30990             2.883492e-09 1.113222e-06       Gm30990
Ablim1|Ablim1               5.444438e-04 4.620058e-02        Ablim1
LOC108168424|LOC108168424   3.676027e-07 5.610225e-05  LOC108168424
Gm33534|Gm33534             1.263313e-08 3.465232e-06       Gm33534
Rnd3|Rnd3                   2.889344e-04 2.740556e-02          Rnd3
Ppp1r1c|Ppp1r1c             6.581433e-13 7.858231e-10       Ppp1r1c
Slc43a3|Slc43a3             1.562973e-07 2.640805e-05       Slc43a3
Actc1|Actc1                 1.248019e-07 2.261811e-05         Actc1
LOC108168839|LOC108168839   2.312412e-04 2.289626e-02  LOC108168839
1810024B03Rik|1810024B03Rik 1.199472e-04 1.268067e-02 1810024B03Rik
Oxt|Oxt                     6.189336e-08 1.196487e-05           Oxt
Gm33648|Gm33648             1.010347e-08 3.107276e-06       Gm33648
Cfap61|Cfap61               6.103542e-10 3.441380e-07        Cfap61
Rprd1b|Rprd1b               3.176894e-05 3.893545e-03        Rprd1b
Npepl1|Npepl1               1.013812e-04 1.088802e-02        Npepl1
Fgf2|Fgf2                   7.523890e-08 1.427289e-05          Fgf2
Ctso|Ctso                   1.783192e-04 1.801888e-02          Ctso
Gm30352|Gm30352             1.455063e-08 3.937984e-06       Gm30352
Ash1l|Ash1l                 4.657116e-04 4.022559e-02         Ash1l
Rorc|Rorc                   9.013284e-06 1.236160e-03          Rorc
Snx27|Snx27                 3.875648e-04 3.538934e-02         Snx27
Setdb1|Setdb1               6.294168e-06 8.934197e-04        Setdb1
Hist2h4|Hist2h4             5.572617e-04 4.646871e-02       Hist2h4
LOC108168896|LOC108168896   1.821021e-04 1.829856e-02  LOC108168896
Gm35408|Gm35408             2.502184e-08 5.839430e-06       Gm35408
LOC108168900|LOC108168900   3.577700e-05 4.322628e-03  LOC108168900
Gm40150|Gm40150             1.275001e-13 2.352724e-10       Gm40150
Emcn|Emcn                   7.687415e-11 5.380660e-08          Emcn
Gm40187|Gm40187             5.436486e-08 1.077197e-05       Gm40187
Ube2r2|Ube2r2               4.615571e-05 5.320334e-03        Ube2r2
Gm38592|Gm38592             4.369165e-04 3.839191e-02       Gm38592
Tusc1|Tusc1                 8.236989e-06 1.145167e-03         Tusc1
Cyp2j12|Cyp2j12             1.246417e-05 1.653580e-03       Cyp2j12
Gm12701|Gm12701             2.803648e-11 2.371185e-08       Gm12701
Mroh7|Mroh7                 5.218069e-05 5.950358e-03         Mroh7
LOC102634683|LOC102634683   1.326740e-07 2.341755e-05  LOC102634683
Ccdc27|Ccdc27               3.037324e-04 2.841088e-02        Ccdc27
Gm42362|Gm42362             1.570044e-07 2.640805e-05       Gm42362
Plekhn1|Plekhn1             3.894828e-04 3.538934e-02       Plekhn1
Gm29868|Gm29868             2.423568e-09 1.024866e-06       Gm29868
Gm5106|Gm5106               2.432087e-15 1.645550e-11        Gm5106
Crot|Crot                   1.164648e-06 1.738236e-04          Crot
Gm15421|Gm15421             2.724003e-04 2.595860e-02       Gm15421
Gm35055|Gm35055             2.504879e-04 2.432729e-02       Gm35055
Gm15614|Gm15614             9.996074e-06 1.352669e-03       Gm15614
Evc|Evc                     6.523004e-05 7.274941e-03           Evc
Lyar|Lyar                   2.437582e-07 3.806003e-05          Lyar
Gm40291|Gm40291             1.235280e-12 1.319669e-09       Gm40291
Gm35394|Gm35394             1.833937e-13 3.087447e-10       Gm35394
Asphd2|Asphd2               1.717409e-05 2.192451e-03        Asphd2
4930515G01Rik|4930515G01Rik 1.163727e-08 3.322268e-06 4930515G01Rik
Ccdc64|Ccdc64               1.440369e-05 1.874141e-03        Ccdc64
Fzd10|Fzd10                 5.729868e-04 4.747137e-02         Fzd10
A330070K13Rik|A330070K13Rik 3.620672e-05 4.348663e-03 A330070K13Rik
Pilra|Pilra                 3.095571e-05 3.854841e-03         Pilra
Pds5b|Pds5b                 2.545766e-05 3.229623e-03         Pds5b
Pole4|Pole4                 1.200681e-06 1.778936e-04         Pole4
5031434C07Rik|5031434C07Rik 2.529626e-08 5.839430e-06 5031434C07Rik
Gm38876|Gm38876             1.178457e-08 3.322268e-06       Gm38876
Mug2|Mug2                   9.799910e-05 1.063736e-02          Mug2
Gm33449|Gm33449             6.982686e-11 5.061948e-08       Gm33449
Olr1|Olr1                   3.553423e-08 7.592355e-06          Olr1
Plbd1|Plbd1                 7.222579e-12 7.330195e-09         Plbd1
Ehd2|Ehd2                   3.905416e-04 3.538934e-02          Ehd2
Ccdc9|Ccdc9                 5.462676e-04 4.620058e-02         Ccdc9
Ceacam2|Ceacam2             1.225774e-04 1.289158e-02       Ceacam2
Zfp607|Zfp607               2.730786e-08 6.091152e-06        Zfp607
Map4k1|Map4k1               3.153258e-09 1.185275e-06        Map4k1
Kctd15|Kctd15               1.495843e-06 2.200190e-04        Kctd15
Il4i1|Il4i1                 1.711838e-05 2.192451e-03         Il4i1
Kctd14|Kctd14               2.300980e-08 5.560155e-06        Kctd14
Hbb-bt|Hbb-bt               2.584206e-04 2.497820e-02        Hbb-bt
Hbb-bs|Hbb-bs               1.152642e-05 1.549426e-03        Hbb-bs
Tpcn2|Tpcn2                 2.685978e-09 1.112653e-06         Tpcn2
Ints10|Ints10               3.486297e-04 3.202029e-02        Ints10
Bst2|Bst2                   3.968014e-05 4.682718e-03          Bst2
Klf1|Klf1                   1.117918e-09 5.402740e-07          Klf1
2310036O22Rik|2310036O22Rik 1.607948e-05 2.078862e-03 2310036O22Rik
Gm32122|Gm32122             2.339391e-04 2.305095e-02       Gm32122
Fhod1|Fhod1                 4.048351e-04 3.652152e-02         Fhod1
Ctcf|Ctcf                   4.152438e-05 4.816353e-03          Ctcf
Calb2|Calb2                 3.184198e-05 3.893545e-03         Calb2
LOC108167554|LOC108167554   1.106088e-08 3.253823e-06  LOC108167554
Osgin1|Osgin1               3.201371e-14 8.122677e-11        Osgin1
Vps9d1|Vps9d1               5.964206e-05 6.725636e-03        Vps9d1
Oaf|Oaf                     4.419553e-13 5.606755e-10           Oaf
Ccdc153|Ccdc153             3.302071e-08 7.207037e-06       Ccdc153
Stra6|Stra6                 1.977378e-13 3.087447e-10         Stra6
Gm39386|Gm39386             4.179568e-08 8.483687e-06       Gm39386
D030055H07Rik|D030055H07Rik 2.451676e-04 2.392506e-02 D030055H07Rik
Manf|Manf                   2.370016e-04 2.323989e-02          Manf
Traip|Traip                 6.021197e-05 6.752389e-03         Traip
Gm38623|Gm38623             4.332411e-04 3.823447e-02       Gm38623
Ubp1|Ubp1                   5.856293e-04 4.832156e-02          Ubp1
Cul4b|Cul4b                 1.139369e-04 1.210833e-02         Cul4b
Stk26|Stk26                 1.224161e-14 4.969602e-11         Stk26
4930502E18Rik|4930502E18Rik 1.642144e-04 1.677624e-02 4930502E18Rik
4933403O08Rik|4933403O08Rik 2.279985e-09 1.024866e-06 4933403O08Rik
Nms|Nms                     1.091279e-12 1.230599e-09           Nms
Gm30900|Gm30900             1.451396e-07 2.539693e-05       Gm30900
Gm41939|Gm41939             4.598695e-09 1.637619e-06       Gm41939
Lamc2|Lamc2                 3.072514e-13 4.157726e-10         Lamc2
4930523C07Rik|4930523C07Rik 4.308055e-09 1.589907e-06 4930523C07Rik
Gm32749|Gm32749             4.011022e-08 8.307727e-06       Gm32749
Gm33377|Gm33377             1.174596e-07 2.167449e-05       Gm33377
Efemp1|Efemp1               3.247651e-06 4.675235e-04        Efemp1
Wnt9a|Wnt9a                 1.780166e-07 2.914017e-05         Wnt9a
Cldn7|Cldn7                 2.853418e-09 1.113222e-06         Cldn7
Rhbdf2|Rhbdf2               8.163962e-12 7.891052e-09        Rhbdf2
LOC108167980|LOC108167980   6.761902e-08 1.294840e-05  LOC108167980
Gm34489|Gm34489             2.704143e-10 1.770603e-07       Gm34489
Gm40375|Gm40375             1.579838e-07 2.640805e-05       Gm40375
Gm40474|Gm40474             4.537672e-04 3.953033e-02       Gm40474
Gm5086|Gm5086               8.269568e-08 1.554219e-05        Gm5086
Gm31452|Gm31452             1.214088e-07 2.220140e-05       Gm31452
Gm30363|Gm30363             4.100597e-08 8.407467e-06       Gm30363
Il17rd|Il17rd               2.116780e-04 2.106196e-02        Il17rd
Mir17hg|Mir17hg             1.548983e-07 2.640805e-05       Mir17hg
Capsl|Capsl                 2.033821e-08 5.160313e-06         Capsl
Gm41447|Gm41447             9.735778e-08 1.812998e-05       Gm41447
Drd3|Drd3                   4.288948e-11 3.246771e-08          Drd3
Rsph1|Rsph1                 2.760894e-09 1.113222e-06         Rsph1
Gpsm3|Gpsm3                 3.211790e-04 2.990501e-02         Gpsm3
Slc22a7|Slc22a7             3.232407e-07 4.970561e-05       Slc22a7
Plin5|Plin5                 1.174623e-08 3.322268e-06         Plin5
Tbc1d10c|Tbc1d10c           6.574056e-09 2.224003e-06      Tbc1d10c
Olfr1417|Olfr1417           2.323643e-06 3.393188e-04      Olfr1417
Fut7|Fut7                   1.814577e-08 4.722088e-06          Fut7
Dbh|Dbh                     7.215575e-10 3.958425e-07           Dbh
Spc25|Spc25                 9.141720e-10 4.757914e-07         Spc25
4833423E24Rik|4833423E24Rik 3.086280e-10 1.845506e-07 4833423E24Rik
Rad51|Rad51                 2.355273e-09 1.024866e-06         Rad51
Cd40|Cd40                   2.164573e-08 5.293555e-06          Cd40
Gm39990|Gm39990             1.283176e-07 2.304948e-05       Gm39990
Helz2|Helz2                 1.587241e-07 2.640805e-05         Helz2
Sprr1a|Sprr1a               2.223327e-14 6.447014e-11        Sprr1a
Hist2h2bb|Hist2h2bb         1.309634e-07 2.331838e-05     Hist2h2bb
Gabrr1|Gabrr1               1.734986e-08 4.573605e-06        Gabrr1
Hspb7|Hspb7                 2.605648e-08 5.942634e-06         Hspb7
Gm32374|Gm32374             1.653272e-08 4.415541e-06       Gm32374
Gm40349|Gm40349             2.531628e-08 5.839430e-06       Gm40349
Vmn1r4|Vmn1r4               3.792779e-08 7.936683e-06        Vmn1r4
Mcm2|Mcm2                   5.113021e-04 4.397631e-02          Mcm2
Lpar5|Lpar5                 9.919232e-12 9.151844e-09         Lpar5
Zfp541|Zfp541               3.402384e-04 3.139163e-02        Zfp541
Rcn3|Rcn3                   1.084183e-08 3.236285e-06          Rcn3
LOC108167437|LOC108167437   5.925383e-04 4.869370e-02  LOC108167437
Gm35021|Gm35021             1.889882e-07 3.068362e-05       Gm35021
Ces5a|Ces5a                 2.359567e-08 5.634647e-06         Ces5a
Il10ra|Il10ra               2.906727e-09 1.113222e-06        Il10ra
Gm15169|Gm15169             2.020180e-09 9.536187e-07       Gm15169
                                                                                                      description
Gm28836|Gm28836                                                                              predicted gene 28836
Vwa3b|Vwa3b                                                          von Willebrand factor A domain containing 3B
4930439A04Rik|4930439A04Rik                                                            RIKEN cDNA 4930439A04 gene
LOC108167622|LOC108167622                                                                                    <NA>
Pard3bos2|Pard3bos2                                  par-3 family cell polarity regulator beta, opposite strand 2
Col4a3|Col4a3                                                                          collagen, type IV, alpha 3
Dnajb3|Dnajb3                                                    DnaJ heat shock protein family (Hsp40) member B3
Asb18|Asb18                                                             ankyrin repeat and SOCS box-containing 18
Gm41920|Gm41920                                                                             predicted gene, 41920
LOC105246710|LOC105246710                                                                                    <NA>
LOC108167732|LOC108167732                                                                                    <NA>
Fam129a|Fam129a                                                                                              <NA>
Fmo1|Fmo1                                                                       flavin containing monooxygenase 1
Gorab|Gorab                                                                              golgin, RAB6-interacting
Dnah14|Dnah14                                                                    dynein, axonemal, heavy chain 14
Atf3|Atf3                                                                       activating transcription factor 3
B230208H11Rik|B230208H11Rik                                                            RIKEN cDNA B230208H11 gene
LOC108167797|LOC108167797                                                                                    <NA>
Fam26f|Fam26f                                                                                                <NA>
Mical1|Mical1                          microtubule associated monooxygenase, calponin and LIM domain containing 1
LOC108167812|LOC108167812                                                                                    <NA>
Upb1|Upb1                                                                                  ureidopropionase, beta
Eid3|Eid3                                                        EP300 interacting inhibitor of differentiation 3
Gm5174|Gm5174                                                                                 predicted gene 5174
Gm32898|Gm32898                                                                             predicted gene, 32898
5730420D15Rik|5730420D15Rik                                                            RIKEN cDNA 5730420D15 gene
Nab2|Nab2                                                                                Ngfi-A binding protein 2
Itga7|Itga7                                                                                      integrin alpha 7
Pkd1l1|Pkd1l1                                                                  polycystic kidney disease 1 like 1
Hba-a1|Hba-a1                                                                     hemoglobin alpha, adult chain 1
Hba-a2|Hba-a2                                                                     hemoglobin alpha, adult chain 2
Maml1|Maml1                                                         mastermind like transcriptional coactivator 1
Zfp354a|Zfp354a                                                                          zinc finger protein 354A
Pemt|Pemt                                                            phosphatidylethanolamine N-methyltransferase
F930015N05Rik|F930015N05Rik                                                            RIKEN cDNA F930015N05 gene
Nxn|Nxn                                                                                             nucleoredoxin
Gm29979|Gm29979                                                                             predicted gene, 29979
Mmp28|Mmp28                                                                 matrix metallopeptidase 28 (epilysin)
Hnf1b|Hnf1b                                                                                       HNF1 homeobox B
Gm525|Gm525                                                                                    predicted gene 525
Rara|Rara                                                                           retinoic acid receptor, alpha
Zfp385c|Zfp385c                                                                          zinc finger protein 385C
Aoc2|Aoc2                                                    amine oxidase, copper containing 2 (retina-specific)
Brca1|Brca1                                                                          breast cancer 1, early onset
Sphk1|Sphk1                                                                                  sphingosine kinase 1
Gen1|Gen1                                                            GEN1, Holliday junction 5' flap endonuclease
Prps1l3|Prps1l3                                                  phosphoribosyl pyrophosphate synthetase 1-like 3
Gm20337|Gm20337                                                                             predicted gene, 20337
Gm38543|Gm38543                                                                             predicted gene, 38543
Gm33682|Gm33682                                                                             predicted gene, 33682
AW209491|AW209491                                                                     expressed sequence AW209491
Hus1b|Hus1b                                                                     HUS1 checkpoint clamp component B
A230103O09Rik|A230103O09Rik                                                            RIKEN cDNA A230103O09 gene
Gm31683|Gm31683                                                                             predicted gene, 31683
Catsper3|Catsper3                                                              cation channel, sperm associated 3
1810034E14Rik|1810034E14Rik                                                            RIKEN cDNA 1810034E14 gene
Exoc3|Exoc3                                                                           exocyst complex component 3
Gm38604|Gm38604                                                                             predicted gene, 38604
3110070M22Rik|3110070M22Rik                                                            RIKEN cDNA 3110070M22 gene
Mmrn2|Mmrn2                                                                                          multimerin 2
Cdhr1|Cdhr1                                                                      cadherin-related family member 1
4930563I02Rik|4930563I02Rik                                                            RIKEN cDNA 4930563I02 gene
Arl11|Arl11                                                                       ADP-ribosylation factor-like 11
Gm35679|Gm35679                                                                             predicted gene, 35679
Samd12|Samd12                                                            sterile alpha motif domain containing 12
Col22a1|Col22a1                                                                      collagen, type XXII, alpha 1
Gm44502|Gm44502                                           predicted readthrough transcript (NMD candidate), 44502
A330009N23Rik|A330009N23Rik                                                            RIKEN cDNA A330009N23 gene
Gm16861|Gm16861                                                                             predicted gene, 16861
Eef2kmt|Eef2kmt                                           eukaryotic elongation factor 2 lysine methyltransferase
Sdf2l1|Sdf2l1                                                                stromal cell-derived factor 2-like 1
Lrrc74b|Lrrc74b                                                                leucine rich repeat containing 74B
Tfrc|Tfrc                                                                                    transferrin receptor
Dopey2|Dopey2                                                                                                <NA>
Gm41523|Gm41523                                                                             predicted gene, 41523
Mas1|Mas1                                                                                           MAS1 oncogene
Tbl3|Tbl3                                                                                transducin (beta)-like 3
Tead3|Tead3                                                                            TEA domain family member 3
Cdkn1a|Cdkn1a                                                          cyclin-dependent kinase inhibitor 1A (P21)
Hsf2bp|Hsf2bp                                                   heat shock transcription factor 2 binding protein
Zfp811|Zfp811                                                                             zinc finger protein 811
H2-K1|H2-K1                                                                    histocompatibility 2, K1, K region
H2-DMa|H2-DMa                                                           histocompatibility 2, class II, locus DMa
Nfkbie|Nfkbie               nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, epsilon
Ebi3|Ebi3                                                                       Epstein-Barr virus induced gene 3
Crb3|Crb3                                                                                  crumbs family member 3
Hnrnpll|Hnrnpll                                                    heterogeneous nuclear ribonucleoprotein L-like
4930543D07Rik|4930543D07Rik                                                            RIKEN cDNA 4930543D07 gene
Ttr|Ttr                                                                                             transthyretin
BC051408|BC051408                                                                          cDNA sequence BC051408
Apbb3|Apbb3                                       amyloid beta (A4) precursor protein-binding, family B, member 3
Dnd1|Dnd1                                                            DND microRNA-mediated repression inhibitor 1
Tex43|Tex43                                                                                   testis expressed 43
Gm41795|Gm41795                                                                             predicted gene, 41795
Ptgdr2|Ptgdr2                                                                         prostaglandin D2 receptor 2
LOC108168412|LOC108168412                                                                                    <NA>
Gm30990|Gm30990                                                                             predicted gene, 30990
Ablim1|Ablim1                                                                         actin-binding LIM protein 1
LOC108168424|LOC108168424                                                                                    <NA>
Gm33534|Gm33534                                                                             predicted gene, 33534
Rnd3|Rnd3                                                                                     Rho family GTPase 3
Ppp1r1c|Ppp1r1c                                            protein phosphatase 1, regulatory inhibitor subunit 1C
Slc43a3|Slc43a3                                                                solute carrier family 43, member 3
Actc1|Actc1                                                                        actin, alpha, cardiac muscle 1
LOC108168839|LOC108168839                                                                                    <NA>
1810024B03Rik|1810024B03Rik                                                            RIKEN cDNA 1810024B03 gene
Oxt|Oxt                                                                                                  oxytocin
Gm33648|Gm33648                                                                             predicted gene, 33648
Cfap61|Cfap61                                                            cilia and flagella associated protein 61
Rprd1b|Rprd1b                                                 regulation of nuclear pre-mRNA domain containing 1B
Npepl1|Npepl1                                                                               aminopeptidase-like 1
Fgf2|Fgf2                                                                              fibroblast growth factor 2
Ctso|Ctso                                                                                             cathepsin O
Gm30352|Gm30352                                                                             predicted gene, 30352
Ash1l|Ash1l                                                            ASH1 like histone lysine methyltransferase
Rorc|Rorc                                                                       RAR-related orphan receptor gamma
Snx27|Snx27                                                                        sorting nexin family member 27
Setdb1|Setdb1                                                                            SET domain, bifurcated 1
Hist2h4|Hist2h4                                                                                              <NA>
LOC108168896|LOC108168896                                                                                    <NA>
Gm35408|Gm35408                                                                             predicted gene, 35408
LOC108168900|LOC108168900                                                                                    <NA>
Gm40150|Gm40150                                                                             predicted gene, 40150
Emcn|Emcn                                                                                               endomucin
Gm40187|Gm40187                                                                             predicted gene, 40187
Ube2r2|Ube2r2                                                                  ubiquitin-conjugating enzyme E2R 2
Gm38592|Gm38592                                                                             predicted gene, 38592
Tusc1|Tusc1                                                                          tumor suppressor candidate 1
Cyp2j12|Cyp2j12                                            cytochrome P450, family 2, subfamily j, polypeptide 12
Gm12701|Gm12701                                                                              predicted gene 12701
Mroh7|Mroh7                                                              maestro heat-like repeat family member 7
LOC102634683|LOC102634683                                                                                    <NA>
Ccdc27|Ccdc27                                                                    coiled-coil domain containing 27
Gm42362|Gm42362                                                                             predicted gene, 42362
Plekhn1|Plekhn1                                          pleckstrin homology domain containing, family N member 1
Gm29868|Gm29868                                                                             predicted gene, 29868
Gm5106|Gm5106                                                                                 predicted gene 5106
Crot|Crot                                                                         carnitine O-octanoyltransferase
Gm15421|Gm15421                                                           ribosomal protein L22 like 1 pseudogene
Gm35055|Gm35055                                                                             predicted gene, 35055
Gm15614|Gm15614                                                                              predicted gene 15614
Evc|Evc                                                                             EvC ciliary complex subunit 1
Lyar|Lyar                                                                             Ly1 antibody reactive clone
Gm40291|Gm40291                                                                             predicted gene, 40291
Gm35394|Gm35394                                                                             predicted gene, 35394
Asphd2|Asphd2                                                      aspartate beta-hydroxylase domain containing 2
4930515G01Rik|4930515G01Rik                                                            RIKEN cDNA 4930515G01 gene
Ccdc64|Ccdc64                                                                                                <NA>
Fzd10|Fzd10                                                                            frizzled class receptor 10
A330070K13Rik|A330070K13Rik                                                            RIKEN cDNA A330070K13 gene
Pilra|Pilra                                                        paired immunoglobin-like type 2 receptor alpha
Pds5b|Pds5b                                                                      PDS5 cohesin associated factor B
Pole4|Pole4                                                    polymerase (DNA-directed), epsilon 4 (p12 subunit)
5031434C07Rik|5031434C07Rik                                                            RIKEN cDNA 5031434C07 gene
Gm38876|Gm38876                                                                             predicted gene, 38876
Mug2|Mug2                                                                                        murinoglobulin 2
Gm33449|Gm33449                                                                             predicted gene, 33449
Olr1|Olr1                                               oxidized low density lipoprotein (lectin-like) receptor 1
Plbd1|Plbd1                                                                   phospholipase B domain containing 1
Ehd2|Ehd2                                                                                  EH-domain containing 2
Ccdc9|Ccdc9                                                                       coiled-coil domain containing 9
Ceacam2|Ceacam2                                                                      CEA cell adhesion molecule 2
Zfp607|Zfp607                                                                                                <NA>
Map4k1|Map4k1                                             mitogen-activated protein kinase kinase kinase kinase 1
Kctd15|Kctd15                                              potassium channel tetramerisation domain containing 15
Il4i1|Il4i1                                                                               interleukin 4 induced 1
Kctd14|Kctd14                                              potassium channel tetramerisation domain containing 14
Hbb-bt|Hbb-bt                                                                      hemoglobin, beta adult t chain
Hbb-bs|Hbb-bs                                                                      hemoglobin, beta adult s chain
Tpcn2|Tpcn2                                                                            two pore segment channel 2
Ints10|Ints10                                                                       integrator complex subunit 10
Bst2|Bst2                                                                      bone marrow stromal cell antigen 2
Klf1|Klf1                                                                       Kruppel-like factor 1 (erythroid)
2310036O22Rik|2310036O22Rik                                                                                  <NA>
Gm32122|Gm32122                                                                             predicted gene, 32122
Fhod1|Fhod1                                                                 formin homology 2 domain containing 1
Ctcf|Ctcf                                                                                    CCCTC-binding factor
Calb2|Calb2                                                                                           calbindin 2
LOC108167554|LOC108167554                                                                                    <NA>
Osgin1|Osgin1                                                         oxidative stress induced growth inhibitor 1
Vps9d1|Vps9d1                                                                            VPS9 domain containing 1
Oaf|Oaf                                                                                      out at first homolog
Ccdc153|Ccdc153                                                                 coiled-coil domain containing 153
Stra6|Stra6                                                                    stimulated by retinoic acid gene 6
Gm39386|Gm39386                                                                             predicted gene, 39386
D030055H07Rik|D030055H07Rik                                                            RIKEN cDNA D030055H07 gene
Manf|Manf                                                     mesencephalic astrocyte-derived neurotrophic factor
Traip|Traip                                                                              TRAF-interacting protein
Gm38623|Gm38623                                                                             predicted gene, 38623
Ubp1|Ubp1                                                                              upstream binding protein 1
Cul4b|Cul4b                                                                                             cullin 4B
Stk26|Stk26                                                                            serine/threonine kinase 26
4930502E18Rik|4930502E18Rik                                                                                  <NA>
4933403O08Rik|4933403O08Rik                                                            RIKEN cDNA 4933403O08 gene
Nms|Nms                                                                                              neuromedin S
Gm30900|Gm30900                                                                             predicted gene, 30900
Gm41939|Gm41939                                                                             predicted gene, 41939
Lamc2|Lamc2                                                                                      laminin, gamma 2
4930523C07Rik|4930523C07Rik                                                            RIKEN cDNA 4930523C07 gene
Gm32749|Gm32749                                                                             predicted gene, 32749
Gm33377|Gm33377                                                                             predicted gene, 33377
Efemp1|Efemp1                      epidermal growth factor-containing fibulin-like extracellular matrix protein 1
Wnt9a|Wnt9a                                                 wingless-type MMTV integration site family, member 9A
Cldn7|Cldn7                                                                                             claudin 7
Rhbdf2|Rhbdf2                                                                                rhomboid 5 homolog 2
LOC108167980|LOC108167980                                                                                    <NA>
Gm34489|Gm34489                                                                             predicted gene, 34489
Gm40375|Gm40375                                                                             predicted gene, 40375
Gm40474|Gm40474                                                                             predicted gene, 40474
Gm5086|Gm5086                                                                                 predicted gene 5086
Gm31452|Gm31452                                                                             predicted gene, 31452
Gm30363|Gm30363                                                                             predicted gene, 30363
Il17rd|Il17rd                                                                           interleukin 17 receptor D
Mir17hg|Mir17hg                                                              Mir17 host gene (non-protein coding)
Capsl|Capsl                                                                                     calcyphosine-like
Gm41447|Gm41447                                                                             predicted gene, 41447
Drd3|Drd3                                                                                    dopamine receptor D3
Rsph1|Rsph1                                                           radial spoke head 1 homolog (Chlamydomonas)
Gpsm3|Gpsm3                                              G-protein signalling modulator 3 (AGS3-like, C. elegans)
Slc22a7|Slc22a7                                    solute carrier family 22 (organic anion transporter), member 7
Plin5|Plin5                                                                                           perilipin 5
Tbc1d10c|Tbc1d10c                                                                  TBC1 domain family, member 10c
Olfr1417|Olfr1417                                                                                            <NA>
Fut7|Fut7                                                                                    fucosyltransferase 7
Dbh|Dbh                                                                                 dopamine beta hydroxylase
Spc25|Spc25                                   SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)
4833423E24Rik|4833423E24Rik                                                                                  <NA>
Rad51|Rad51                                                                                     RAD51 recombinase
Cd40|Cd40                                                                                            CD40 antigen
Gm39990|Gm39990                                                                             predicted gene, 39990
Helz2|Helz2                                              helicase with zinc finger 2, transcriptional coactivator
Sprr1a|Sprr1a                                                                       small proline-rich protein 1A
Hist2h2bb|Hist2h2bb                                                                                          <NA>
Gabrr1|Gabrr1                                            gamma-aminobutyric acid (GABA) C receptor, subunit rho 1
Hspb7|Hspb7                                                  heat shock protein family, member 7 (cardiovascular)
Gm32374|Gm32374                                                                             predicted gene, 32374
Gm40349|Gm40349                                                                             predicted gene, 40349
Vmn1r4|Vmn1r4                                                                            vomeronasal 1 receptor 4
Mcm2|Mcm2                                                          minichromosome maintenance complex component 2
Lpar5|Lpar5                                                                      lysophosphatidic acid receptor 5
Zfp541|Zfp541                                                                             zinc finger protein 541
Rcn3|Rcn3                                                        reticulocalbin 3, EF-hand calcium binding domain
LOC108167437|LOC108167437                                                                                    <NA>
Gm35021|Gm35021                                                                             predicted gene, 35021
Ces5a|Ces5a                                                                                   carboxylesterase 5A
Il10ra|Il10ra                                                                      interleukin 10 receptor, alpha
Gm15169|Gm15169                                                                              predicted gene 15169
                               entrez      ensembl             Comparison
Gm28836|Gm28836             102635593           NA Craving vs FoodTrained
Vwa3b|Vwa3b                     70853 ENSMUSG0.... Craving vs FoodTrained
4930439A04Rik|4930439A04Rik     78119           NA Craving vs FoodTrained
LOC108167622|LOC108167622        <NA>              Craving vs FoodTrained
Pard3bos2|Pard3bos2         105243940 ENSMUSG0.... Craving vs FoodTrained
Col4a3|Col4a3                   12828 ENSMUSG0.... Craving vs FoodTrained
Dnajb3|Dnajb3                   15504 ENSMUSG0.... Craving vs FoodTrained
Asb18|Asb18                    208372 ENSMUSG0.... Craving vs FoodTrained
Gm41920|Gm41920             105246666           NA Craving vs FoodTrained
LOC105246710|LOC105246710        <NA>              Craving vs FoodTrained
LOC108167732|LOC108167732        <NA>              Craving vs FoodTrained
Fam129a|Fam129a                  <NA>              Craving vs FoodTrained
Fmo1|Fmo1                       14261 ENSMUSG0.... Craving vs FoodTrained
Gorab|Gorab                     98376 ENSMUSG0.... Craving vs FoodTrained
Dnah14|Dnah14                  240960 ENSMUSG0.... Craving vs FoodTrained
Atf3|Atf3                       11910 ENSMUSG0.... Craving vs FoodTrained
B230208H11Rik|B230208H11Rik    320273 ENSMUSG0.... Craving vs FoodTrained
LOC108167797|LOC108167797        <NA>              Craving vs FoodTrained
Fam26f|Fam26f                    <NA>              Craving vs FoodTrained
Mical1|Mical1                  171580 ENSMUSG0.... Craving vs FoodTrained
LOC108167812|LOC108167812        <NA>              Craving vs FoodTrained
Upb1|Upb1                      103149 ENSMUSG0.... Craving vs FoodTrained
Eid3|Eid3                       66341 ENSMUSG0.... Craving vs FoodTrained
Gm5174|Gm5174                  382395 ENSMUSG0.... Craving vs FoodTrained
Gm32898|Gm32898             102635607           NA Craving vs FoodTrained
5730420D15Rik|5730420D15Rik     70523 ENSMUSG0.... Craving vs FoodTrained
Nab2|Nab2                       17937 ENSMUSG0.... Craving vs FoodTrained
Itga7|Itga7                     16404 ENSMUSG0.... Craving vs FoodTrained
Pkd1l1|Pkd1l1                  171395 ENSMUSG0.... Craving vs FoodTrained
Hba-a1|Hba-a1                   15122 ENSMUSG0.... Craving vs FoodTrained
Hba-a2|Hba-a2                  110257 ENSMUSG0.... Craving vs FoodTrained
Maml1|Maml1                    103806 ENSMUSG0.... Craving vs FoodTrained
Zfp354a|Zfp354a                 21408 ENSMUSG0.... Craving vs FoodTrained
Pemt|Pemt                       18618 ENSMUSG0.... Craving vs FoodTrained
F930015N05Rik|F930015N05Rik    654805           NA Craving vs FoodTrained
Nxn|Nxn                         18230 ENSMUSG0.... Craving vs FoodTrained
Gm29979|Gm29979             102631709           NA Craving vs FoodTrained
Mmp28|Mmp28                    118453 ENSMUSG0.... Craving vs FoodTrained
Hnf1b|Hnf1b                     21410 ENSMUSG0.... Craving vs FoodTrained
Gm525|Gm525                    217071 ENSMUSG0.... Craving vs FoodTrained
Rara|Rara                       19401 ENSMUSG0.... Craving vs FoodTrained
Zfp385c|Zfp385c                278304 ENSMUSG0.... Craving vs FoodTrained
Aoc2|Aoc2                      237940 ENSMUSG0.... Craving vs FoodTrained
Brca1|Brca1                     12189 ENSMUSG0.... Craving vs FoodTrained
Sphk1|Sphk1                     20698 ENSMUSG0.... Craving vs FoodTrained
Gen1|Gen1                      209334 ENSMUSG0.... Craving vs FoodTrained
Prps1l3|Prps1l3                328099 ENSMUSG0.... Craving vs FoodTrained
Gm20337|Gm20337             100504661           NA Craving vs FoodTrained
Gm38543|Gm38543             102641236           NA Craving vs FoodTrained
Gm33682|Gm33682             102636679           NA Craving vs FoodTrained
AW209491|AW209491              105351 ENSMUSG0.... Craving vs FoodTrained
Hus1b|Hus1b                    210554 ENSMUSG0.... Craving vs FoodTrained
A230103O09Rik|A230103O09Rik     77753 ENSMUSG0.... Craving vs FoodTrained
Gm31683|Gm31683             102633993           NA Craving vs FoodTrained
Catsper3|Catsper3               76856 ENSMUSG0.... Craving vs FoodTrained
1810034E14Rik|1810034E14Rik     66503 ENSMUSG0.... Craving vs FoodTrained
Exoc3|Exoc3                    211446 ENSMUSG0.... Craving vs FoodTrained
Gm38604|Gm38604             102642321           NA Craving vs FoodTrained
3110070M22Rik|3110070M22Rik     67304 ENSMUSG0.... Craving vs FoodTrained
Mmrn2|Mmrn2                    105450 ENSMUSG0.... Craving vs FoodTrained
Cdhr1|Cdhr1                    170677 ENSMUSG0.... Craving vs FoodTrained
4930563I02Rik|4930563I02Rik     67659           NA Craving vs FoodTrained
Arl11|Arl11                    219144 ENSMUSG0.... Craving vs FoodTrained
Gm35679|Gm35679             102639345           NA Craving vs FoodTrained
Samd12|Samd12                  320679 ENSMUSG0.... Craving vs FoodTrained
Col22a1|Col22a1                 69700 ENSMUSG0.... Craving vs FoodTrained
Gm44502|Gm44502             100134861 ENSMUSG0.... Craving vs FoodTrained
A330009N23Rik|A330009N23Rik    380977 ENSMUSG0.... Craving vs FoodTrained
Gm16861|Gm16861             100503704 ENSMUSG0.... Craving vs FoodTrained
Eef2kmt|Eef2kmt                 70511 ENSMUSG0.... Craving vs FoodTrained
Sdf2l1|Sdf2l1                   64136 ENSMUSG0.... Craving vs FoodTrained
Lrrc74b|Lrrc74b                 74685 ENSMUSG0.... Craving vs FoodTrained
Tfrc|Tfrc                       22042 ENSMUSG0.... Craving vs FoodTrained
Dopey2|Dopey2                    <NA>              Craving vs FoodTrained
Gm41523|Gm41523             105246190           NA Craving vs FoodTrained
Mas1|Mas1                       17171 ENSMUSG0.... Craving vs FoodTrained
Tbl3|Tbl3                      213773 ENSMUSG0.... Craving vs FoodTrained
Tead3|Tead3                     21678 ENSMUSG0.... Craving vs FoodTrained
Cdkn1a|Cdkn1a                   12575 ENSMUSG0.... Craving vs FoodTrained
Hsf2bp|Hsf2bp                   74377 ENSMUSG0.... Craving vs FoodTrained
Zfp811|Zfp811                  240063 ENSMUSG0.... Craving vs FoodTrained
H2-K1|H2-K1                     14972 ENSMUSG0.... Craving vs FoodTrained
H2-DMa|H2-DMa                   14998 ENSMUSG0.... Craving vs FoodTrained
Nfkbie|Nfkbie                   18037 ENSMUSG0.... Craving vs FoodTrained
Ebi3|Ebi3                       50498 ENSMUSG0.... Craving vs FoodTrained
Crb3|Crb3                      224912 ENSMUSG0.... Craving vs FoodTrained
Hnrnpll|Hnrnpll                 72692 ENSMUSG0.... Craving vs FoodTrained
4930543D07Rik|4930543D07Rik     75176           NA Craving vs FoodTrained
Ttr|Ttr                         22139 ENSMUSG0.... Craving vs FoodTrained
BC051408|BC051408              408061 ENSMUSG0.... Craving vs FoodTrained
Apbb3|Apbb3                    225372 ENSMUSG0.... Craving vs FoodTrained
Dnd1|Dnd1                      213236 ENSMUSG0.... Craving vs FoodTrained
Tex43|Tex43                     67343 ENSMUSG0.... Craving vs FoodTrained
Gm41795|Gm41795             105246514           NA Craving vs FoodTrained
Ptgdr2|Ptgdr2                   14764 ENSMUSG0.... Craving vs FoodTrained
LOC108168412|LOC108168412        <NA>              Craving vs FoodTrained
Gm30990|Gm30990             102633075           NA Craving vs FoodTrained
Ablim1|Ablim1                  226251 ENSMUSG0.... Craving vs FoodTrained
LOC108168424|LOC108168424        <NA>              Craving vs FoodTrained
Gm33534|Gm33534             102636479           NA Craving vs FoodTrained
Rnd3|Rnd3                       74194 ENSMUSG0.... Craving vs FoodTrained
Ppp1r1c|Ppp1r1c                 75276 ENSMUSG0.... Craving vs FoodTrained
Slc43a3|Slc43a3                 58207 ENSMUSG0.... Craving vs FoodTrained
Actc1|Actc1                     11464 ENSMUSG0.... Craving vs FoodTrained
LOC108168839|LOC108168839        <NA>              Craving vs FoodTrained
1810024B03Rik|1810024B03Rik    329509 ENSMUSG0.... Craving vs FoodTrained
Oxt|Oxt                         18429 ENSMUSG0.... Craving vs FoodTrained
Gm33648|Gm33648             102636639           NA Craving vs FoodTrained
Cfap61|Cfap61                   78774 ENSMUSG0.... Craving vs FoodTrained
Rprd1b|Rprd1b                   70470 ENSMUSG0.... Craving vs FoodTrained
Npepl1|Npepl1                  228961 ENSMUSG0.... Craving vs FoodTrained
Fgf2|Fgf2                       14173 ENSMUSG0.... Craving vs FoodTrained
Ctso|Ctso                      229445 ENSMUSG0.... Craving vs FoodTrained
Gm30352|Gm30352             102632212           NA Craving vs FoodTrained
Ash1l|Ash1l                    192195 ENSMUSG0.... Craving vs FoodTrained
Rorc|Rorc                       19885 ENSMUSG0.... Craving vs FoodTrained
Snx27|Snx27                     76742 ENSMUSG0.... Craving vs FoodTrained
Setdb1|Setdb1                   84505 ENSMUSG0.... Craving vs FoodTrained
Hist2h4|Hist2h4                  <NA>              Craving vs FoodTrained
LOC108168896|LOC108168896        <NA>              Craving vs FoodTrained
Gm35408|Gm35408             102638976           NA Craving vs FoodTrained
LOC108168900|LOC108168900        <NA>              Craving vs FoodTrained
Gm40150|Gm40150             105244557           NA Craving vs FoodTrained
Emcn|Emcn                       59308 ENSMUSG0.... Craving vs FoodTrained
Gm40187|Gm40187             105244597           NA Craving vs FoodTrained
Ube2r2|Ube2r2                   67615 ENSMUSG0.... Craving vs FoodTrained
Gm38592|Gm38592             102642011           NA Craving vs FoodTrained
Tusc1|Tusc1                     69136 ENSMUSG0.... Craving vs FoodTrained
Cyp2j12|Cyp2j12                242546 ENSMUSG0.... Craving vs FoodTrained
Gm12701|Gm12701             105244634           NA Craving vs FoodTrained
Mroh7|Mroh7                    381538 ENSMUSG0.... Craving vs FoodTrained
LOC102634683|LOC102634683        <NA>              Craving vs FoodTrained
Ccdc27|Ccdc27                  381580 ENSMUSG0.... Craving vs FoodTrained
Gm42362|Gm42362             105247228           NA Craving vs FoodTrained
Plekhn1|Plekhn1                231002 ENSMUSG0.... Craving vs FoodTrained
Gm29868|Gm29868             102631562           NA Craving vs FoodTrained
Gm5106|Gm5106                  330031 ENSMUSG0.... Craving vs FoodTrained
Crot|Crot                       74114 ENSMUSG0.... Craving vs FoodTrained
Gm15421|Gm15421             100042049           NA Craving vs FoodTrained
Gm35055|Gm35055             102638509           NA Craving vs FoodTrained
Gm15614|Gm15614             102640951 ENSMUSG0.... Craving vs FoodTrained
Evc|Evc                         59056 ENSMUSG0.... Craving vs FoodTrained
Lyar|Lyar                       17089 ENSMUSG0.... Craving vs FoodTrained
Gm40291|Gm40291             105244734           NA Craving vs FoodTrained
Gm35394|Gm35394             102638959 ENSMUSG0.... Craving vs FoodTrained
Asphd2|Asphd2                   72898 ENSMUSG0.... Craving vs FoodTrained
4930515G01Rik|4930515G01Rik     67642 ENSMUSG0.... Craving vs FoodTrained
Ccdc64|Ccdc64                    <NA>              Craving vs FoodTrained
Fzd10|Fzd10                     93897 ENSMUSG0.... Craving vs FoodTrained
A330070K13Rik|A330070K13Rik    381673 ENSMUSG0.... Craving vs FoodTrained
Pilra|Pilra                    231805 ENSMUSG0.... Craving vs FoodTrained
Pds5b|Pds5b                    100710 ENSMUSG0.... Craving vs FoodTrained
Pole4|Pole4                     66979 ENSMUSG0.... Craving vs FoodTrained
5031434C07Rik|5031434C07Rik 100503613           NA Craving vs FoodTrained
Gm38876|Gm38876             105242742           NA Craving vs FoodTrained
Mug2|Mug2                       17837 ENSMUSG0.... Craving vs FoodTrained
Gm33449|Gm33449             102636362           NA Craving vs FoodTrained
Olr1|Olr1                      108078 ENSMUSG0.... Craving vs FoodTrained
Plbd1|Plbd1                     66857 ENSMUSG0.... Craving vs FoodTrained
Ehd2|Ehd2                      259300 ENSMUSG0.... Craving vs FoodTrained
Ccdc9|Ccdc9                    243846 ENSMUSG0.... Craving vs FoodTrained
Ceacam2|Ceacam2                 26367 ENSMUSG0.... Craving vs FoodTrained
Zfp607|Zfp607                    <NA>              Craving vs FoodTrained
Map4k1|Map4k1                   26411 ENSMUSG0.... Craving vs FoodTrained
Kctd15|Kctd15                  233107 ENSMUSG0.... Craving vs FoodTrained
Il4i1|Il4i1                     14204 ENSMUSG0.... Craving vs FoodTrained
Kctd14|Kctd14                  233529 ENSMUSG0.... Craving vs FoodTrained
Hbb-bt|Hbb-bt               101488143 ENSMUSG0.... Craving vs FoodTrained
Hbb-bs|Hbb-bs               100503605 ENSMUSG0.... Craving vs FoodTrained
Tpcn2|Tpcn2                    233979 ENSMUSG0.... Craving vs FoodTrained
Ints10|Ints10                   70885 ENSMUSG0.... Craving vs FoodTrained
Bst2|Bst2                       69550 ENSMUSG0.... Craving vs FoodTrained
Klf1|Klf1                       16596 ENSMUSG0.... Craving vs FoodTrained
2310036O22Rik|2310036O22Rik      <NA>              Craving vs FoodTrained
Gm32122|Gm32122             102634575 ENSMUSG0.... Craving vs FoodTrained
Fhod1|Fhod1                    234686 ENSMUSG0.... Craving vs FoodTrained
Ctcf|Ctcf                       13018 ENSMUSG0.... Craving vs FoodTrained
Calb2|Calb2                     12308 ENSMUSG0.... Craving vs FoodTrained
LOC108167554|LOC108167554        <NA>              Craving vs FoodTrained
Osgin1|Osgin1                   71839 ENSMUSG0.... Craving vs FoodTrained
Vps9d1|Vps9d1                   72325 ENSMUSG0.... Craving vs FoodTrained
Oaf|Oaf                        102644 ENSMUSG0.... Craving vs FoodTrained
Ccdc153|Ccdc153                270150 ENSMUSG0.... Craving vs FoodTrained
Stra6|Stra6                     20897 ENSMUSG0.... Craving vs FoodTrained
Gm39386|Gm39386             105243472           NA Craving vs FoodTrained
D030055H07Rik|D030055H07Rik    654798           NA Craving vs FoodTrained
Manf|Manf                       74840 ENSMUSG0.... Craving vs FoodTrained
Traip|Traip                     22036 ENSMUSG0.... Craving vs FoodTrained
Gm38623|Gm38623             102642652           NA Craving vs FoodTrained
Ubp1|Ubp1                       22221 ENSMUSG0.... Craving vs FoodTrained
Cul4b|Cul4b                     72584 ENSMUSG0.... Craving vs FoodTrained
Stk26|Stk26                     70415 ENSMUSG0.... Craving vs FoodTrained
4930502E18Rik|4930502E18Rik      <NA>              Craving vs FoodTrained
4933403O08Rik|4933403O08Rik     71030 ENSMUSG0.... Craving vs FoodTrained
Nms|Nms                        433292 ENSMUSG0.... Craving vs FoodTrained
Gm30900|Gm30900             102632958           NA Craving vs FoodTrained
Gm41939|Gm41939             105246691           NA Craving vs FoodTrained
Lamc2|Lamc2                     16782 ENSMUSG0.... Craving vs FoodTrained
4930523C07Rik|4930523C07Rik     67647 ENSMUSG0.... Craving vs FoodTrained
Gm32749|Gm32749             102635396           NA Craving vs FoodTrained
Gm33377|Gm33377             102636263           NA Craving vs FoodTrained
Efemp1|Efemp1                  216616 ENSMUSG0.... Craving vs FoodTrained
Wnt9a|Wnt9a                    216795 ENSMUSG0.... Craving vs FoodTrained
Cldn7|Cldn7                     53624 ENSMUSG0.... Craving vs FoodTrained
Rhbdf2|Rhbdf2                  217344 ENSMUSG0.... Craving vs FoodTrained
LOC108167980|LOC108167980        <NA>              Craving vs FoodTrained
Gm34489|Gm34489             102637759           NA Craving vs FoodTrained
Gm40375|Gm40375             105244840           NA Craving vs FoodTrained
Gm40474|Gm40474             105244956           NA Craving vs FoodTrained
Gm5086|Gm5086                  328314 ENSMUSG0.... Craving vs FoodTrained
Gm31452|Gm31452             102633689           NA Craving vs FoodTrained
Gm30363|Gm30363             102632228           NA Craving vs FoodTrained
Il17rd|Il17rd                  171463 ENSMUSG0.... Craving vs FoodTrained
Mir17hg|Mir17hg                 75957           NA Craving vs FoodTrained
Capsl|Capsl                     75568 ENSMUSG0.... Craving vs FoodTrained
Gm41447|Gm41447             105246104           NA Craving vs FoodTrained
Drd3|Drd3                       13490 ENSMUSG0.... Craving vs FoodTrained
Rsph1|Rsph1                     22092 ENSMUSG0.... Craving vs FoodTrained
Gpsm3|Gpsm3                    106512 ENSMUSG0.... Craving vs FoodTrained
Slc22a7|Slc22a7                108114 ENSMUSG0.... Craving vs FoodTrained
Plin5|Plin5                     66968 ENSMUSG0.... Craving vs FoodTrained
Tbc1d10c|Tbc1d10c              108995 ENSMUSG0.... Craving vs FoodTrained
Olfr1417|Olfr1417                <NA>              Craving vs FoodTrained
Fut7|Fut7                       14347 ENSMUSG0.... Craving vs FoodTrained
Dbh|Dbh                         13166 ENSMUSG0.... Craving vs FoodTrained
Spc25|Spc25                     66442 ENSMUSG0.... Craving vs FoodTrained
4833423E24Rik|4833423E24Rik      <NA>              Craving vs FoodTrained
Rad51|Rad51                     19361 ENSMUSG0.... Craving vs FoodTrained
Cd40|Cd40                       21939 ENSMUSG0.... Craving vs FoodTrained
Gm39990|Gm39990             105244367           NA Craving vs FoodTrained
Helz2|Helz2                    229003 ENSMUSG0.... Craving vs FoodTrained
Sprr1a|Sprr1a                   20753 ENSMUSG0.... Craving vs FoodTrained
Hist2h2bb|Hist2h2bb              <NA>              Craving vs FoodTrained
Gabrr1|Gabrr1                   14408 ENSMUSG0.... Craving vs FoodTrained
Hspb7|Hspb7                     29818 ENSMUSG0.... Craving vs FoodTrained
Gm32374|Gm32374             102634899           NA Craving vs FoodTrained
Gm40349|Gm40349             105244804           NA Craving vs FoodTrained
Vmn1r4|Vmn1r4                  171194 ENSMUSG0.... Craving vs FoodTrained
Mcm2|Mcm2                       17216 ENSMUSG0.... Craving vs FoodTrained
Lpar5|Lpar5                    381810 ENSMUSG0.... Craving vs FoodTrained
Zfp541|Zfp541                  666528 ENSMUSG0.... Craving vs FoodTrained
Rcn3|Rcn3                       52377 ENSMUSG0.... Craving vs FoodTrained
LOC108167437|LOC108167437        <NA>              Craving vs FoodTrained
Gm35021|Gm35021             102638463 ENSMUSG0.... Craving vs FoodTrained
Ces5a|Ces5a                     67935 ENSMUSG0.... Craving vs FoodTrained
Il10ra|Il10ra                   16154 ENSMUSG0.... Craving vs FoodTrained
Gm15169|Gm15169             105243737           NA Craving vs FoodTrained

log2 fold change (MLE): condition Maintenance vs FoodTrained 
Wald test p-value: condition Maintenance vs FoodTrained 
DataFrame with 35976 rows and 10 columns
                           baseMean log2FoldChange     lfcSE       stat
                          <numeric>      <numeric> <numeric>  <numeric>
Mrpl15|Mrpl15             2162.2677       0.658955  0.370756  1.7773286
Gm39587|Gm39587             20.3013      -1.761961  3.625839 -0.4859458
Lypla1|Lypla1              994.9024       0.091420  0.940712  0.0971817
Xkr4|Xkr4                 4459.4285       0.634191  0.290259  2.1849118
Gm39585|Gm39585           5797.3848       1.179803  0.258007  4.5727554
...                             ...            ...       ...        ...
Gm28300|Gm28300                   0             NA        NA         NA
Gm28301|Gm28301                   0             NA        NA         NA
LOC100861691|LOC100861691         0             NA        NA         NA
LOC102639451|LOC102639451         0             NA        NA         NA
LOC102639672|LOC102639672         0             NA        NA         NA
                               pvalue        padj       symbol
                            <numeric>   <numeric>  <character>
Mrpl15|Mrpl15             7.55142e-02 0.378210047       Mrpl15
Gm39587|Gm39587           6.27006e-01 0.934572124      Gm39587
Lypla1|Lypla1             9.22582e-01 0.994937072       Lypla1
Xkr4|Xkr4                 2.88953e-02 0.218091109         Xkr4
Gm39585|Gm39585           4.81352e-06 0.000197302      Gm39585
...                               ...         ...          ...
Gm28300|Gm28300                    NA          NA      Gm28300
Gm28301|Gm28301                    NA          NA      Gm28301
LOC100861691|LOC100861691          NA          NA LOC100861691
LOC102639451|LOC102639451          NA          NA LOC102639451
LOC102639672|LOC102639672          NA          NA LOC102639672
                                     description      entrez            ensembl
                                     <character> <character>             <list>
Mrpl15|Mrpl15             mitochondrial riboso..       27395 ENSMUSG00000033845
Gm39587|Gm39587                               NA          NA                   
Lypla1|Lypla1                lysophospholipase 1       18777 ENSMUSG00000025903
Xkr4|Xkr4                 X-linked Kx blood gr..      497097 ENSMUSG00000051951
Gm39585|Gm39585            predicted gene, 39585   105243853                 NA
...                                          ...         ...                ...
Gm28300|Gm28300             predicted gene 28300   105247288                 NA
Gm28301|Gm28301             predicted gene 28301   102635002                 NA
LOC100861691|LOC100861691 X-linked lymphocyte-..   100861691 ENSMUSG00000100485
LOC102639451|LOC102639451                     NA          NA                   
LOC102639672|LOC102639672                     NA          NA                   

log2 fold change (MLE): condition Craving vs Maintenance 
Wald test p-value: condition Craving vs Maintenance 
DataFrame with 35976 rows and 10 columns
                           baseMean log2FoldChange     lfcSE       stat
                          <numeric>      <numeric> <numeric>  <numeric>
Mrpl15|Mrpl15             2162.2677     -0.2627261  0.346645 -0.7579115
Gm39587|Gm39587             20.3013     -0.3516955  3.397661 -0.1035111
Lypla1|Lypla1              994.9024     -0.0715356  0.879922 -0.0812976
Xkr4|Xkr4                 4459.4285     -0.6679818  0.271480 -2.4605151
Gm39585|Gm39585           5797.3848     -1.0936780  0.241281 -4.5327985
...                             ...            ...       ...        ...
Gm28300|Gm28300                   0             NA        NA         NA
Gm28301|Gm28301                   0             NA        NA         NA
LOC100861691|LOC100861691         0             NA        NA         NA
LOC102639451|LOC102639451         0             NA        NA         NA
LOC102639672|LOC102639672         0             NA        NA         NA
                               pvalue        padj       symbol
                            <numeric>   <numeric>  <character>
Mrpl15|Mrpl15             4.48504e-01 0.865132253       Mrpl15
Gm39587|Gm39587           9.17557e-01 0.993925150      Gm39587
Lypla1|Lypla1             9.35205e-01 0.995172062       Lypla1
Xkr4|Xkr4                 1.38738e-02 0.149517036         Xkr4
Gm39585|Gm39585           5.82073e-06 0.000274895      Gm39585
...                               ...         ...          ...
Gm28300|Gm28300                    NA          NA      Gm28300
Gm28301|Gm28301                    NA          NA      Gm28301
LOC100861691|LOC100861691          NA          NA LOC100861691
LOC102639451|LOC102639451          NA          NA LOC102639451
LOC102639672|LOC102639672          NA          NA LOC102639672
                                     description      entrez            ensembl
                                     <character> <character>             <list>
Mrpl15|Mrpl15             mitochondrial riboso..       27395 ENSMUSG00000033845
Gm39587|Gm39587                               NA          NA                   
Lypla1|Lypla1                lysophospholipase 1       18777 ENSMUSG00000025903
Xkr4|Xkr4                 X-linked Kx blood gr..      497097 ENSMUSG00000051951
Gm39585|Gm39585            predicted gene, 39585   105243853                 NA
...                                          ...         ...                ...
Gm28300|Gm28300             predicted gene 28300   105247288                 NA
Gm28301|Gm28301             predicted gene 28301   102635002                 NA
LOC100861691|LOC100861691 X-linked lymphocyte-..   100861691 ENSMUSG00000100485
LOC102639451|LOC102639451                     NA          NA                   
LOC102639672|LOC102639672                     NA          NA                   

Past versions of "Volcano Plots-1.png"

Version	Author	Date
a1c090c	avm27	2024-07-17

5.5.2 Visualize Results: Volcano Plots (Interactive)

Interactive Volcano plots are generated by Using the same method as above, but are plotted so that genes may be identified and log2FC can be seen from each gene. Plots can be used to customize which genes appear based on what you would like to see.

Session information

sessionInfo()

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] plotly_4.10.2                            
 [2] gridExtra_2.3                            
 [3] ggrepel_0.9.3                            
 [4] BiocParallel_1.32.6                      
 [5] conflicted_1.2.0                         
 [6] VennDiagram_1.7.3                        
 [7] futile.logger_1.4.3                      
 [8] regionReport_1.32.0                      
 [9] kableExtra_1.3.4                         
[10] vidger_1.18.0                            
[11] tables_0.9.17                            
[12] knitr_1.43                               
[13] Glimma_2.8.0                             
[14] Mus.musculus_1.3.1                       
[15] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0
[16] OrganismDbi_1.40.0                       
[17] GenomicFeatures_1.50.4                   
[18] gplots_3.1.3                             
[19] lubridate_1.9.2                          
[20] forcats_1.0.0                            
[21] stringr_1.5.1                            
[22] purrr_1.0.2                              
[23] readr_2.1.4                              
[24] tibble_3.2.1                             
[25] tidyverse_2.0.0                          
[26] statmod_1.5.0                            
[27] tweeDEseqCountData_1.36.0                
[28] edgeR_3.40.2                             
[29] limma_3.54.2                             
[30] GOSemSim_2.24.0                          
[31] apeglm_1.20.0                            
[32] ggpubr_0.6.0                             
[33] SPIA_2.50.0                              
[34] KEGGgraph_1.58.3                         
[35] ggnewscale_0.4.9                         
[36] enrichplot_1.18.4                        
[37] tidyr_1.3.1                              
[38] WGCNA_1.72-1                             
[39] fastcluster_1.2.3                        
[40] dynamicTreeCut_1.63-1                    
[41] pathview_1.38.0                          
[42] gage_2.48.0                              
[43] dplyr_1.1.4                              
[44] topGO_2.50.0                             
[45] SparseM_1.81                             
[46] graph_1.76.0                             
[47] GO.db_3.16.0                             
[48] RColorBrewer_1.1-3                       
[49] genefilter_1.80.3                        
[50] pheatmap_1.0.12                          
[51] ggsci_3.0.0                              
[52] tximport_1.26.1                          
[53] org.Mm.eg.db_3.16.0                      
[54] AnnotationDbi_1.60.2                     
[55] DOSE_3.24.2                              
[56] ReactomePA_1.42.0                        
[57] biomaRt_2.54.1                           
[58] clusterProfiler_4.6.2                    
[59] ggplot2_3.5.0.9000                       
[60] DESeq2_1.38.3                            
[61] SummarizedExperiment_1.28.0              
[62] Biobase_2.58.0                           
[63] MatrixGenerics_1.10.0                    
[64] matrixStats_1.0.0                        
[65] GenomicRanges_1.50.2                     
[66] GenomeInfoDb_1.34.9                      
[67] IRanges_2.32.0                           
[68] S4Vectors_0.36.2                         
[69] BiocGenerics_0.44.0                      
[70] gprofiler2_0.2.2                         
[71] workflowr_1.7.0                          

loaded via a namespace (and not attached):
  [1] Hmisc_5.1-0              svglite_2.1.1            ps_1.7.5                
  [4] Rsamtools_2.14.0         foreach_1.5.2            rprojroot_2.0.3         
  [7] crayon_1.5.2             MASS_7.3-60              nlme_3.1-162            
 [10] backports_1.4.1          impute_1.72.3            rlang_1.1.3             
 [13] XVector_0.38.0           HDO.db_0.99.1            callr_3.7.3             
 [16] filelock_1.0.2           rjson_0.2.21             bit64_4.0.5             
 [19] glue_1.7.0               rngtools_1.5.2           parallel_4.2.1          
 [22] processx_3.8.2           DEFormats_1.26.0         tidyselect_1.2.1        
 [25] XML_3.99-0.14            GenomicAlignments_1.34.1 xtable_1.8-4            
 [28] magrittr_2.0.3           evaluate_0.21            bibtex_0.5.1            
 [31] cli_3.6.2                zlibbioc_1.44.0          doRNG_1.8.6             
 [34] rstudioapi_0.14          whisker_0.4.1            bslib_0.5.0             
 [37] rpart_4.1.19             derfinderHelper_1.32.0   fastmatch_1.1-3         
 [40] BiocStyle_2.26.0         lambda.r_1.2.4           treeio_1.22.0           
 [43] xfun_0.39                gson_0.1.0               cluster_2.1.4           
 [46] caTools_1.18.2           tidygraph_1.2.3          KEGGREST_1.38.0         
 [49] ape_5.7-1                Biostrings_2.66.0        png_0.1-8               
 [52] reshape_0.8.9            withr_3.0.0              bitops_1.0-7            
 [55] ggforce_0.4.1            RBGL_1.74.0              plyr_1.8.8              
 [58] coda_0.19-4              bumphunter_1.40.0        pillar_1.9.0            
 [61] cachem_1.0.8             fs_1.6.2                 graphite_1.44.0         
 [64] ellipsis_0.3.2           vctrs_0.6.5              generics_0.1.3          
 [67] tools_4.2.1              foreign_0.8-84           munsell_0.5.1           
 [70] tweenr_2.0.2             fgsea_1.24.0             DelayedArray_0.24.0     
 [73] fastmap_1.1.1            compiler_4.2.1           abind_1.4-5             
 [76] httpuv_1.6.11            rtracklayer_1.58.0       GenomeInfoDbData_1.2.9  
 [79] lattice_0.21-8           utf8_1.2.4               later_1.3.1             
 [82] BiocFileCache_2.6.1      jsonlite_1.8.7           GGally_2.1.2            
 [85] scales_1.3.0             tidytree_0.4.2           carData_3.0-5           
 [88] lazyeval_0.2.2           promises_1.2.0.1         car_3.1-2               
 [91] doParallel_1.0.17        checkmate_2.2.0          rmarkdown_2.23          
 [94] cowplot_1.1.1            webshot_0.5.5            downloader_0.4          
 [97] BSgenome_1.66.3          igraph_1.5.0             survival_3.5-5          
[100] numDeriv_2016.8-1.1      yaml_2.3.7               systemfonts_1.0.4       
[103] htmltools_0.5.5          memoise_2.0.1            VariantAnnotation_1.44.1
[106] BiocIO_1.8.0             locfit_1.5-9.8           graphlayouts_1.0.0      
[109] viridisLite_0.4.2        digest_0.6.32            rappdirs_0.3.3          
[112] knitrBootstrap_1.0.2     futile.options_1.0.1     emdbook_1.3.13          
[115] RSQLite_2.3.1            yulab.utils_0.0.6        derfinder_1.32.0        
[118] data.table_1.14.8        blob_1.2.4               preprocessCore_1.60.2   
[121] labeling_0.4.3           splines_4.2.1            Formula_1.2-5           
[124] RCurl_1.98-1.12          broom_1.0.5              hms_1.1.3               
[127] colorspace_2.1-0         base64enc_0.1-3          BiocManager_1.30.21     
[130] aplot_0.1.10             nnet_7.3-19              sass_0.4.6              
[133] Rcpp_1.0.10              mvtnorm_1.2-2            fansi_1.0.6             
[136] tzdb_0.4.0               R6_2.5.1                 lifecycle_1.0.4         
[139] formatR_1.14             curl_5.0.1               ggsignif_0.6.4          
[142] jquerylib_0.1.4          Matrix_1.5-4.1           qvalue_2.30.0           
[145] org.Hs.eg.db_3.16.0      iterators_1.0.14         RefManageR_1.4.0        
[148] htmlwidgets_1.6.2        markdown_1.7             polyclip_1.10-4         
[151] crosstalk_1.2.0          shadowtext_0.1.2         timechange_0.2.0        
[154] gridGraphics_0.5-1       reactome.db_1.82.0       rvest_1.0.3             
[157] htmlTable_2.4.1          patchwork_1.2.0.9000     bdsmatrix_1.3-6         
[160] codetools_0.2-19         gtools_3.9.4             getPass_0.2-2           
[163] prettyunits_1.1.1        dbplyr_2.3.2             gtable_0.3.5            
[166] DBI_1.1.3                git2r_0.32.0             ggfun_0.1.1             
[169] httr_1.4.6               highr_0.10               KernSmooth_2.23-21      
[172] stringi_1.8.4            progress_1.2.2           reshape2_1.4.4          
[175] farver_2.1.2             annotate_1.76.0          viridis_0.6.3           
[178] Rgraphviz_2.42.0         ggtree_3.6.2             xml2_1.3.4              
[181] bbmle_1.0.25             restfulr_0.0.15          geneplotter_1.76.0      
[184] ggplotify_0.1.1          bit_4.0.5                scatterpie_0.2.1        
[187] ggraph_2.1.0             pkgconfig_2.0.3          rstatix_0.7.2           
[190] GenomicFiles_1.34.0